Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-06 23:55 -0500 (Sat, 06 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4879
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4668
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/31HostnameOS / ArchCHECK
biodbNcbi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-12-06 09:55 -0500 (Sat, 06 Dec 2025)
git_url: https://git.bioconductor.org/packages/biodbNcbi
git_branch: RELEASE_3_22
git_last_commit: dc1f90a
git_last_commit_date: 2025-10-29 11:15:40 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNcbi on merida1

To the developers/maintainers of the biodbNcbi package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbNcbi
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
StartedAt: 2025-12-06 16:01:29 -0500 (Sat, 06 Dec 2025)
EndedAt: 2025-12-06 16:02:46 -0500 (Sat, 06 Dec 2025)
EllapsedTime: 77.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNcbi.Rcheck
Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2025-12-06 16:02:33.641][biodb::testContext]
biodb.INFO [2025-12-06 16:02:33.645][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:33.646][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-12-06 16:02:33.647][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:33.649][biodb::testContext]
biodb.INFO [2025-12-06 16:02:33.656][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:33.658][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:33.666][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:33.667][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-06 16:02:33.669][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-06 16:02:33.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.674][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-06 16:02:33.700][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-06 16:02:33.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.714][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-06 16:02:33.715][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-06 16:02:33.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.720][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-06 16:02:33.721][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-06 16:02:33.722][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-06 16:02:33.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.727][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-06 16:02:33.728][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-06 16:02:33.730][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-06 16:02:33.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.734][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-06 16:02:33.736][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-06 16:02:33.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.740][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-06 16:02:33.741][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-06 16:02:33.743][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-06 16:02:33.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.747][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-06 16:02:33.749][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-06 16:02:33.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.753][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-06 16:02:33.754][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-06 16:02:33.756][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-06 16:02:33.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.760][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:33.761][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-06 16:02:33.763][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-06 16:02:33.764][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-06 16:02:33.765][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-06 16:02:33.767][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-06 16:02:33.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.771][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-06 16:02:33.772][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-06 16:02:33.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.777][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-06 16:02:33.778][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-06 16:02:33.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.783][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-06 16:02:33.784][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-06 16:02:33.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.789][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-06 16:02:33.790][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-06 16:02:33.791][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-06 16:02:33.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.796][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:33.797][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-06 16:02:33.807][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-06 16:02:33.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.812][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-06 16:02:33.813][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-06 16:02:33.815][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-06 16:02:33.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:33.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:33.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:33.822][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-06 16:02:33.865][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.886][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-06 16:02:33.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:33.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.895][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:33.896][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:33.898][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.899][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-06 16:02:33.900][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:33.901][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.903][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.904][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:33.904][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:33.904][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:33.904][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:33.904][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:33.905][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:33.906][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:33.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:33.909][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:33.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:33.911][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:33.912][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.913][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.915][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:33.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:33.917][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.918][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.920][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-06 16:02:33.922][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.923][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:33.924][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.926][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:33.927][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.932][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.935][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.936][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:33.937][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:33.939][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.940][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-06 16:02:33.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:33.942][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.943][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.945][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:33.945][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:33.945][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:33.945][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:33.945][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:33.946][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:33.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:33.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:33.949][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:33.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:33.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:33.953][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.954][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.955][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:33.956][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:33.957][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.959][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.960][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-06 16:02:33.962][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.964][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-06 16:02:33.965][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.966][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:33.967][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.968][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.970][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.971][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.972][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:33.973][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:33.975][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.976][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-06 16:02:33.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:33.978][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.979][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:33.981][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.982][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:33.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:33.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:33.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:33.987][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:33.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:33.989][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:33.990][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.991][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:33.992][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:33.993][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:33.995][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:33.996][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-06 16:02:33.998][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.000][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:34.001][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:34.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.005][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.006][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:34.007][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.008][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:34.010][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:34.011][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:34.012][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-06 16:02:34.013][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:34.014][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:34.016][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.017][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:34.018][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:34.019][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.022][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:34.023][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.025][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.027][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:34.028][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:34.029][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:34.030][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:34.031][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:34.035][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:34.036][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.128][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-06 16:02:34.133][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-06 16:02:34.135][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-06 16:02:34.136][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-06 16:02:34.142][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-06 16:02:34.144][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:02:34.146][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:34.147][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:34.149][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-06 16:02:34.151][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:02:34.152][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:02:34.154][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-06 16:02:34.156][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:34.158][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:34.159][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:34.161][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:34.163][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-06 16:02:34.164][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-06 16:02:34.166][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-06 16:02:34.168][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-06 16:02:34.169][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-06 16:02:34.171][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-06 16:02:34.173][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-06 16:02:34.174][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-06 16:02:34.176][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-06 16:02:34.178][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-06 16:02:34.180][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-06 16:02:34.181][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-06 16:02:34.183][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-06 16:02:34.185][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-06 16:02:34.186][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-06 16:02:34.188][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-06 16:02:34.190][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-06 16:02:34.191][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-06 16:02:34.193][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-06 16:02:34.195][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-06 16:02:34.196][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-06 16:02:34.198][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-06 16:02:34.200][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-06 16:02:34.202][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-06 16:02:34.203][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-06 16:02:34.205][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-06 16:02:34.207][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-06 16:02:34.208][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-06 16:02:34.210][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-06 16:02:34.212][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:34.213][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-06 16:02:34.215][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-06 16:02:34.217][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-06 16:02:34.219][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-06 16:02:34.220][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-06 16:02:34.222][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-06 16:02:34.224][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-06 16:02:34.225][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-06 16:02:34.227][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-06 16:02:34.229][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-06 16:02:34.231][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-06 16:02:34.232][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-06 16:02:34.234][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-06 16:02:34.236][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-06 16:02:34.238][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-06 16:02:34.239][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-06 16:02:34.241][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-06 16:02:34.243][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-06 16:02:34.245][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-06 16:02:34.247][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-06 16:02:34.248][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-06 16:02:34.250][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-06 16:02:34.252][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-06 16:02:34.253][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-06 16:02:34.255][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-06 16:02:34.257][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-06 16:02:34.258][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-06 16:02:34.260][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-06 16:02:34.262][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-06 16:02:34.263][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-06 16:02:34.265][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-06 16:02:34.267][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-06 16:02:34.268][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-06 16:02:34.270][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-06 16:02:34.272][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-06 16:02:34.273][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-06 16:02:34.275][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-06 16:02:34.283][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-06 16:02:34.285][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:34.288][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:34.289][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.291][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:34.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:34.428][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:34.441][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-06 16:02:34.443][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.444][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-06 16:02:34.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.447][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:34.448][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.449][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.450][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.452][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.453][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-06 16:02:34.454][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:34.455][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.457][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-06 16:02:34.458][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:34.459][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-06 16:02:34.459][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-06 16:02:34.461][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:34.462][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:34.463][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:34.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.467][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:34.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.470][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.471][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-06 16:02:34.471][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-06 16:02:34.472][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:34.474][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:34.475][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.476][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:34.477][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-06 16:02:34.480][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.481][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-06 16:02:34.482][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:34.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.487][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.490][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:34.491][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:34.492][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.493][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-06 16:02:34.494][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:34.496][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-06 16:02:34.496][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-06 16:02:34.496][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-06 16:02:34.496][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-06 16:02:34.496][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-06 16:02:34.496][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-06 16:02:34.497][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:34.498][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:34.499][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:34.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.503][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:34.504][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.505][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.506][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.508][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:34.508][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:34.509][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:34.510][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:34.511][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.512][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:34.514][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-06 16:02:34.516][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:34.518][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-06 16:02:34.519][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.520][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:34.521][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.522][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.524][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.525][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.526][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:34.527][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:34.529][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.530][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-06 16:02:34.531][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.532][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:34.538][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:34.539][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:34.539][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:34.539][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:34.541][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-06 16:02:34.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:34.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.547][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.549][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:34.549][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:34.549][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-06 16:02:34.550][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:34.551][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:34.552][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.553][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-06 16:02:34.555][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-06 16:02:34.557][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.559][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-06 16:02:34.560][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.561][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:34.562][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.563][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.565][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.567][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:34.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:34.570][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.571][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-06 16:02:34.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:34.573][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-06 16:02:34.573][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-06 16:02:34.574][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:34.576][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:34.577][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-06 16:02:34.578][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.581][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:34.582][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:34.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:34.584][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:34.585][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:34.585][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:34.585][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-06 16:02:34.587][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:34.588][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:34.589][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:34.590][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-06 16:02:34.598][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-06 16:02:34.600][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:34.602][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:34.604][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-06 16:02:34.606][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:34.608][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-06 16:02:34.628][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-12-06 16:02:34.644][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-12-06 16:02:34.654][biodb::testThat]
biodb.INFO [2025-12-06 16:02:34.655][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-06 16:02:34.656][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:34.657][biodb::testThat]
biodb.TRACE[2025-12-06 16:02:34.662][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-12-06 16:02:34.664][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:02:34.668][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-12-06 16:02:34.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:02:34.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:34.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:34.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:34.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:34.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:34.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-06 16:02:34.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:34.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:34.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.740][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:34.757][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:34.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.759][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.806][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:34.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:34.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.811][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:34.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:34.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.816][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:34.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:34.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:34.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:34.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.826][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:34.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:34.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:34.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:34.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:34.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:34.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:34.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:34.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:34.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:34.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:34.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:34.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:34.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:34.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:34.909][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-12-06 16:02:34.912][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:34.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:34.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.918][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:34.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:34.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:34.996][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:34.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:34.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.001][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:35.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:35.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.006][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:35.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:35.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.011][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:35.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:35.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.040][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.084][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.089][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.095][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.129][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.131][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.133][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.150][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:35.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.156][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.161][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.166][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:35.167][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.170][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.171][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:35.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.187][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.188][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.191][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.198][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.199][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.201][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.226][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-12-06 16:02:35.275][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:02:35.277][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-12-06 16:02:35.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:02:35.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:35.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:35.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:35.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:35.294][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:35.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-06 16:02:35.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.339][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:35.341][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.343][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.345][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:35.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.350][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.355][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.366][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:35.402][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-12-06 16:02:35.429][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.435][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.440][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:35.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:35.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.449][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:35.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:35.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.454][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:35.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:35.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.459][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:35.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:35.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.475][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.519][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.524][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.529][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:35.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.571][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.573][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.575][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.592][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:35.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.597][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.602][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.607][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:35.609][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.611][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.617][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-06 16:02:35.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.633][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.634][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:35.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.637][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:35.643][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:35.644][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:35.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:35.647][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:02:35.657][biodb::testThat]
biodb.INFO [2025-12-06 16:02:35.658][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-06 16:02:35.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:35.661][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:35.664][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-12-06 16:02:35.666][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-12-06 16:02:35.670][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-06 16:02:35.672][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:35.673][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-06 16:02:35.675][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:35.676][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-06 16:02:35.861][biodb::testThat]
biodb.INFO [2025-12-06 16:02:35.863][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-06 16:02:35.864][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:35.865][biodb::testThat]
biodb.INFO [2025-12-06 16:02:35.873][biodb::testThat]
biodb.INFO [2025-12-06 16:02:35.875][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-06 16:02:35.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:35.877][biodb::testThat]
biodb.WARN [2025-12-06 16:02:35.902][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-06 16:02:35.934][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-06 16:02:35.946][biodb::testThat]
biodb.INFO [2025-12-06 16:02:35.947][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-06 16:02:35.948][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:35.949][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:35.973][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-12-06 16:02:36.037][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:36.082][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-06 16:02:36.084][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:36.085][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-06 16:02:36.086][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:36.087][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-06 16:02:36.183][biodb::testThat]
biodb.INFO [2025-12-06 16:02:36.184][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-06 16:02:36.185][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:36.186][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-06 16:02:36.245][biodb::testThat]
biodb.INFO [2025-12-06 16:02:36.246][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-06 16:02:36.247][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:36.248][biodb::testThat]
biodb.INFO [2025-12-06 16:02:36.258][biodb::testThat]
biodb.INFO [2025-12-06 16:02:36.260][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:36.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:36.262][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-06 16:02:36.367][biodb::testThat]
biodb.INFO [2025-12-06 16:02:36.368][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:36.370][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:36.371][biodb::testThat]
biodb.INFO [2025-12-06 16:02:36.379][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-06 16:02:36.381][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-12-06 16:02:36.382][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-06 16:02:36.383][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:36.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:36.385][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.388][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-06 16:02:36.402][biodb::testContext]
biodb.INFO [2025-12-06 16:02:36.404][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:36.405][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-12-06 16:02:36.406][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:36.408][biodb::testContext]
biodb.INFO [2025-12-06 16:02:36.410][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:36.412][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:36.416][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:36.417][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-06 16:02:36.419][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-06 16:02:36.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.423][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-06 16:02:36.425][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-06 16:02:36.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.429][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-06 16:02:36.431][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-06 16:02:36.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.435][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-06 16:02:36.437][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-06 16:02:36.438][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-06 16:02:36.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.443][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-06 16:02:36.444][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-06 16:02:36.445][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-06 16:02:36.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.450][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-06 16:02:36.451][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-06 16:02:36.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.456][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-06 16:02:36.457][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-06 16:02:36.458][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-06 16:02:36.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.463][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-06 16:02:36.464][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-06 16:02:36.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.468][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-06 16:02:36.470][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-06 16:02:36.471][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-06 16:02:36.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.475][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:36.477][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-06 16:02:36.478][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-06 16:02:36.479][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-06 16:02:36.480][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-06 16:02:36.482][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-06 16:02:36.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.486][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-06 16:02:36.487][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-06 16:02:36.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.492][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-06 16:02:36.493][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-06 16:02:36.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.502][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-06 16:02:36.504][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-06 16:02:36.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.508][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-06 16:02:36.509][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-06 16:02:36.511][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-06 16:02:36.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.515][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:36.517][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-06 16:02:36.527][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-06 16:02:36.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.531][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-06 16:02:36.533][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-06 16:02:36.534][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-06 16:02:36.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.539][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-06 16:02:36.541][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.542][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-06 16:02:36.544][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.545][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:36.546][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.547][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.549][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.550][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.551][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:36.552][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:36.554][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.555][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-06 16:02:36.556][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:36.558][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.559][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.560][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:36.560][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:36.560][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:36.560][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:36.560][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:36.561][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:36.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:36.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:36.565][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:36.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:36.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:36.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.570][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.572][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:36.573][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:36.574][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.575][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.577][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-06 16:02:36.579][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.581][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:36.582][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.583][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:36.585][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.586][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.588][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.589][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.590][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:36.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:36.593][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.594][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-06 16:02:36.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:36.597][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.600][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:36.600][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:36.600][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:36.600][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:36.600][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:36.601][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:36.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:36.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:36.605][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:36.606][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:36.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:36.608][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.609][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.611][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:36.612][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:36.613][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.614][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.616][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-06 16:02:36.618][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.619][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-06 16:02:36.621][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.622][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:36.623][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.624][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.626][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.627][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.628][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:36.629][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:36.631][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.632][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-06 16:02:36.633][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:36.635][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.636][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.637][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.638][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:36.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:36.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:36.642][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:36.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:36.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:36.646][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.647][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.648][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:36.649][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:36.650][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.656][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.658][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-06 16:02:36.660][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.661][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:36.662][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:36.665][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.666][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.667][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.668][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.670][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:36.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:36.672][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.674][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-06 16:02:36.675][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:36.676][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.677][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:36.679][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.680][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:36.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:36.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:36.683][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:36.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:36.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:36.687][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:36.688][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.689][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:36.691][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:36.692][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:36.693][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:36.695][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:36.696][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.789][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-06 16:02:36.791][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-06 16:02:36.797][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-06 16:02:36.799][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-06 16:02:36.801][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-06 16:02:36.803][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:02:36.805][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:36.807][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:36.809][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-06 16:02:36.811][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:02:36.812][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:02:36.814][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-06 16:02:36.816][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:36.818][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:36.820][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:36.821][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:36.823][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-06 16:02:36.825][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-06 16:02:36.826][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-06 16:02:36.828][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-06 16:02:36.830][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-06 16:02:36.832][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-06 16:02:36.833][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-06 16:02:36.835][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-06 16:02:36.837][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-06 16:02:36.839][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-06 16:02:36.840][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-06 16:02:36.842][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-06 16:02:36.844][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-06 16:02:36.845][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-06 16:02:36.847][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-06 16:02:36.849][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-06 16:02:36.851][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-06 16:02:36.852][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-06 16:02:36.854][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-06 16:02:36.856][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-06 16:02:36.857][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-06 16:02:36.859][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-06 16:02:36.861][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-06 16:02:36.863][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-06 16:02:36.865][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-06 16:02:36.866][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-06 16:02:36.868][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-06 16:02:36.870][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-06 16:02:36.873][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-06 16:02:36.874][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:36.876][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-06 16:02:36.878][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-06 16:02:36.880][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-06 16:02:36.881][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-06 16:02:36.883][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-06 16:02:36.885][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-06 16:02:36.887][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-06 16:02:36.889][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-06 16:02:36.890][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-06 16:02:36.892][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-06 16:02:36.894][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-06 16:02:36.896][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-06 16:02:36.897][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-06 16:02:36.899][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-06 16:02:36.901][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-06 16:02:36.903][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-06 16:02:36.905][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-06 16:02:36.907][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-06 16:02:36.908][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-06 16:02:36.910][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-06 16:02:36.912][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-06 16:02:36.914][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-06 16:02:36.915][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-06 16:02:36.917][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-06 16:02:36.919][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-06 16:02:36.920][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-06 16:02:36.922][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-06 16:02:36.924][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-06 16:02:36.926][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-06 16:02:36.927][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-06 16:02:36.929][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-06 16:02:36.931][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-06 16:02:36.933][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-06 16:02:36.940][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-06 16:02:36.942][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-06 16:02:36.943][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-06 16:02:36.945][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-06 16:02:36.947][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-06 16:02:36.949][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:36.950][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:36.951][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.954][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:36.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:36.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:36.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:36.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:36.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:36.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:36.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:36.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:36.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:36.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:36.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:36.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:36.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:36.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:36.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:36.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:36.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:37.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:37.089][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:37.091][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-06 16:02:37.094][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.095][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-06 16:02:37.097][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.098][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:37.099][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.100][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.102][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.103][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.104][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-06 16:02:37.106][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:37.107][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.108][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-06 16:02:37.110][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:37.111][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-06 16:02:37.111][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-06 16:02:37.112][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:37.114][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:37.115][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:37.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:37.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:37.119][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:37.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:37.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:37.123][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.124][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-06 16:02:37.124][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-06 16:02:37.125][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:37.126][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:37.128][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.129][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:37.131][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-06 16:02:37.133][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.135][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-06 16:02:37.136][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.137][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:37.138][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.140][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.141][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.142][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.144][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:37.145][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:37.146][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.147][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-06 16:02:37.149][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:37.150][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-06 16:02:37.150][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-06 16:02:37.150][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-06 16:02:37.150][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-06 16:02:37.150][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-06 16:02:37.150][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-06 16:02:37.151][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:37.152][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:37.154][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:37.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:37.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:37.157][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:37.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:37.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:37.161][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.162][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:37.162][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:37.163][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:37.165][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:37.166][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.167][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:37.169][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-06 16:02:37.171][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:37.172][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-06 16:02:37.174][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.175][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:37.176][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.177][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.179][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.180][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.181][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:37.182][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:37.184][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.185][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-06 16:02:37.186][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.187][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:37.189][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:37.190][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:37.190][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:37.190][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:37.191][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-06 16:02:37.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:37.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:37.195][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:37.196][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:37.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:37.198][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.200][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:37.200][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:37.200][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-06 16:02:37.201][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:37.202][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:37.204][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.205][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-06 16:02:37.206][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-06 16:02:37.209][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.210][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-06 16:02:37.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:37.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.216][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.223][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:37.224][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:37.226][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.227][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-06 16:02:37.228][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:37.229][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-06 16:02:37.229][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-06 16:02:37.231][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:37.232][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:37.233][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-06 16:02:37.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:37.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:37.237][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:37.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:37.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:37.240][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:37.241][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:37.241][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:37.241][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-06 16:02:37.243][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:37.244][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:37.245][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:37.246][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-06 16:02:37.248][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-06 16:02:37.250][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:37.252][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:37.253][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-06 16:02:37.255][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:37.257][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-06 16:02:37.266][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-12-06 16:02:37.309][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-12-06 16:02:37.314][biodb::testThat]
biodb.INFO [2025-12-06 16:02:37.316][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-06 16:02:37.317][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:37.318][biodb::testThat]
biodb.TRACE[2025-12-06 16:02:37.324][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-12-06 16:02:37.326][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:02:37.329][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-12-06 16:02:37.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:02:37.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:37.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:37.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:37.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:37.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:37.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-06 16:02:37.358][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.360][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.362][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.369][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:37.371][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:37.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.380][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.382][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-06 16:02:37.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-06 16:02:37.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.388][ef$get] Asked field names are: location.
biodb.TRACE[2025-12-06 16:02:37.389][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-12-06 16:02:37.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.392][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.394][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-12-06 16:02:37.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-12-06 16:02:37.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.400][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-12-06 16:02:37.401][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-12-06 16:02:37.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.403][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.405][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-12-06 16:02:37.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-12-06 16:02:37.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.411][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-12-06 16:02:37.412][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:37.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.414][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.417][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-12-06 16:02:37.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:37.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.422][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-12-06 16:02:37.423][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-12-06 16:02:37.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.425][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.428][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-12-06 16:02:37.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-12-06 16:02:37.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.438][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:37.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:37.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.443][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-06 16:02:37.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-06 16:02:37.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.448][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-06 16:02:37.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-06 16:02:37.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.459][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-06 16:02:37.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-06 16:02:37.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:37.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:37.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:37.494][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-12-06 16:02:37.497][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:37.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:37.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.502][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:37.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:37.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.508][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:37.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:37.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.513][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:37.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:37.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:37.524][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:37.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:37.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:37.529][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-12-06 16:02:37.571][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-12-06 16:02:37.591][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-12-06 16:02:37.593][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-12-06 16:02:37.595][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:37.597][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-06 16:02:37.598][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:37.600][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-06 16:02:37.601][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:37.602][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-06 16:02:37.668][biodb::testThat]
biodb.INFO [2025-12-06 16:02:37.669][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-06 16:02:37.670][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:37.672][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:37.675][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-12-06 16:02:37.676][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-12-06 16:02:37.678][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-06 16:02:37.680][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:37.681][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:37.682][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:37.684][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:37.685][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-06 16:02:37.756][biodb::testThat]
biodb.INFO [2025-12-06 16:02:37.757][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-06 16:02:37.759][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:37.760][biodb::testThat]
biodb.TRACE[2025-12-06 16:02:37.764][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:37.765][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:37.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:37.768][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:37.769][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-12-06 16:02:37.785][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-06 16:02:37.787][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:37.789][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-06 16:02:37.790][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:37.791][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:37.793][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:37.794][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:37.819][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-06 16:02:37.906][biodb::testThat]
biodb.INFO [2025-12-06 16:02:37.908][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-06 16:02:37.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:37.910][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:37.920][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-06 16:02:37.922][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:37.923][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-06 16:02:37.925][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:37.926][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:37.927][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:37.928][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:37.930][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-06 16:02:37.991][biodb::testThat]
biodb.INFO [2025-12-06 16:02:37.992][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-06 16:02:37.993][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:37.994][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:37.999][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-06 16:02:38.001][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:38.003][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-06 16:02:38.004][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:38.005][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:38.006][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:38.007][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:38.009][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-06 16:02:38.090][biodb::testThat]
biodb.INFO [2025-12-06 16:02:38.091][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-06 16:02:38.093][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:38.094][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-06 16:02:38.159][biodb::testThat]
biodb.INFO [2025-12-06 16:02:38.160][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-06 16:02:38.161][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:38.162][biodb::testThat]
biodb.INFO [2025-12-06 16:02:38.172][biodb::testThat]
biodb.INFO [2025-12-06 16:02:38.174][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:38.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:38.176][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-06 16:02:38.235][biodb::testThat]
biodb.INFO [2025-12-06 16:02:38.236][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:38.238][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:38.239][biodb::testThat]
biodb.INFO [2025-12-06 16:02:38.247][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-06 16:02:38.249][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-12-06 16:02:38.250][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-12-06 16:02:38.251][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-06 16:02:38.252][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.255][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.257][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-06 16:02:38.263][biodb::testContext]
biodb.INFO [2025-12-06 16:02:38.264][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:38.265][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-12-06 16:02:38.267][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:38.268][biodb::testContext]
biodb.INFO [2025-12-06 16:02:38.270][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:38.272][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:38.277][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:38.278][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-06 16:02:38.279][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-06 16:02:38.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.289][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-06 16:02:38.291][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-06 16:02:38.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.295][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-06 16:02:38.297][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-06 16:02:38.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.301][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-06 16:02:38.302][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-06 16:02:38.304][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-06 16:02:38.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.308][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-06 16:02:38.310][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-06 16:02:38.311][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-06 16:02:38.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.316][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-06 16:02:38.317][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-06 16:02:38.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.321][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-06 16:02:38.323][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-06 16:02:38.324][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-06 16:02:38.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.329][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-06 16:02:38.330][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-06 16:02:38.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.335][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-06 16:02:38.336][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-06 16:02:38.337][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-06 16:02:38.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.342][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:38.344][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-06 16:02:38.345][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-06 16:02:38.346][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-06 16:02:38.347][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-06 16:02:38.349][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-06 16:02:38.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.353][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-06 16:02:38.354][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-06 16:02:38.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.359][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-06 16:02:38.360][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-06 16:02:38.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.365][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-06 16:02:38.366][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-06 16:02:38.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.371][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-06 16:02:38.372][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-06 16:02:38.373][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-06 16:02:38.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.378][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:38.379][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-06 16:02:38.390][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-06 16:02:38.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.394][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-06 16:02:38.396][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-06 16:02:38.397][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-06 16:02:38.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.402][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-06 16:02:38.404][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.405][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-06 16:02:38.407][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.408][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:38.409][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.410][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.412][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.413][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.414][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:38.416][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:38.419][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.420][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-06 16:02:38.422][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:38.424][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.427][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.431][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:38.431][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:38.431][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:38.431][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:38.431][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:38.434][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:38.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:38.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:38.449][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:38.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:38.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:38.458][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.461][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.464][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:38.466][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:38.469][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.472][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.475][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-06 16:02:38.479][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.482][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:38.484][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.487][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:38.489][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.491][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.494][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.496][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.499][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:38.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:38.504][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.507][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-06 16:02:38.510][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:38.512][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.515][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.518][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:38.518][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:38.518][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:38.518][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:38.518][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:38.521][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:38.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:38.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:38.528][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:38.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:38.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:38.536][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.538][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:38.543][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:38.545][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.548][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.551][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-06 16:02:38.554][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.557][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-06 16:02:38.559][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.562][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:38.564][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.567][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.569][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.571][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.573][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:38.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:38.576][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.578][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-06 16:02:38.581][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:38.583][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.585][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.587][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.588][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:38.589][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:38.590][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:38.592][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:38.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:38.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:38.595][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.596][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.598][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:38.599][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:38.600][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.601][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.603][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-06 16:02:38.605][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.606][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:38.607][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.608][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:38.610][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.612][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.613][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.615][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:38.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:38.617][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.618][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-06 16:02:38.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:38.621][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.622][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:38.623][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.624][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:38.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:38.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:38.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:38.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:38.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:38.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:38.633][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.634][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:38.635][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:38.636][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:38.637][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:38.639][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:38.640][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.734][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-06 16:02:38.736][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-06 16:02:38.738][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-06 16:02:38.739][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-06 16:02:38.741][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-06 16:02:38.743][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:02:38.744][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:38.746][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:38.748][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-06 16:02:38.750][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:02:38.751][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:02:38.753][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-06 16:02:38.755][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:38.756][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:38.758][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:38.760][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:38.761][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-06 16:02:38.763][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-06 16:02:38.765][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-06 16:02:38.770][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-06 16:02:38.772][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-06 16:02:38.774][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-06 16:02:38.776][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-06 16:02:38.777][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-06 16:02:38.779][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-06 16:02:38.781][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-06 16:02:38.782][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-06 16:02:38.784][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-06 16:02:38.786][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-06 16:02:38.787][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-06 16:02:38.789][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-06 16:02:38.791][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-06 16:02:38.792][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-06 16:02:38.794][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-06 16:02:38.796][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-06 16:02:38.797][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-06 16:02:38.799][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-06 16:02:38.801][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-06 16:02:38.803][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-06 16:02:38.804][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-06 16:02:38.806][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-06 16:02:38.808][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-06 16:02:38.809][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-06 16:02:38.811][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-06 16:02:38.813][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-06 16:02:38.814][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:38.816][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-06 16:02:38.818][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-06 16:02:38.819][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-06 16:02:38.821][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-06 16:02:38.823][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-06 16:02:38.824][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-06 16:02:38.826][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-06 16:02:38.828][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-06 16:02:38.830][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-06 16:02:38.831][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-06 16:02:38.833][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-06 16:02:38.835][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-06 16:02:38.836][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-06 16:02:38.838][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-06 16:02:38.840][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-06 16:02:38.842][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-06 16:02:38.843][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-06 16:02:38.845][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-06 16:02:38.847][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-06 16:02:38.848][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-06 16:02:38.850][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-06 16:02:38.852][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-06 16:02:38.854][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-06 16:02:38.855][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-06 16:02:38.857][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-06 16:02:38.859][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-06 16:02:38.860][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-06 16:02:38.862][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-06 16:02:38.864][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-06 16:02:38.865][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-06 16:02:38.867][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-06 16:02:38.869][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-06 16:02:38.870][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-06 16:02:38.872][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-06 16:02:38.874][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-06 16:02:38.875][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-06 16:02:38.877][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-06 16:02:38.879][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-06 16:02:38.881][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:38.882][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:38.883][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.885][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:38.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:38.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:38.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:38.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:38.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:38.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:38.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:39.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:39.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:39.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:39.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:39.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:39.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:39.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:39.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:39.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:39.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:39.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:39.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:39.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:39.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:39.021][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:39.023][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-06 16:02:39.025][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.027][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-06 16:02:39.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.029][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:39.030][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.031][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.033][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.034][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.035][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-06 16:02:39.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:39.038][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.039][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-06 16:02:39.040][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:39.041][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-06 16:02:39.041][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-06 16:02:39.043][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:39.044][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:39.045][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:39.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:39.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:39.048][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:39.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:39.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:39.052][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.053][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-06 16:02:39.053][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-06 16:02:39.054][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:39.055][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:39.057][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.058][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:39.059][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-06 16:02:39.062][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.063][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-06 16:02:39.064][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.065][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:39.066][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.068][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.069][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.070][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.071][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:39.073][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:39.074][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.075][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-06 16:02:39.076][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:39.078][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-06 16:02:39.078][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-06 16:02:39.078][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-06 16:02:39.078][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-06 16:02:39.078][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-06 16:02:39.078][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-06 16:02:39.079][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:39.080][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:39.081][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:39.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:39.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:39.085][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:39.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:39.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:39.088][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.089][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:39.089][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:39.091][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:39.092][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:39.093][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.094][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:39.096][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-06 16:02:39.098][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:39.099][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-06 16:02:39.101][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.102][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:39.103][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.104][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.105][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.107][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.108][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:39.109][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:39.110][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.112][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-06 16:02:39.113][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.114][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:39.116][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:39.117][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:39.117][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:39.117][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:39.118][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-06 16:02:39.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:39.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:39.122][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:39.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:39.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:39.125][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.126][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:39.126][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:39.126][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-06 16:02:39.128][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:39.129][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:39.130][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.131][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-06 16:02:39.133][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-06 16:02:39.135][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.136][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-06 16:02:39.137][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:39.140][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.141][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.142][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.148][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.149][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:39.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:39.152][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.153][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-06 16:02:39.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:39.155][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-06 16:02:39.155][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-06 16:02:39.157][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:39.158][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:39.159][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-06 16:02:39.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:39.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:39.163][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:39.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:39.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:39.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:39.167][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:39.167][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:39.167][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-06 16:02:39.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:39.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:39.171][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:39.172][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-06 16:02:39.174][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-06 16:02:39.176][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:39.178][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:39.182][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-06 16:02:39.185][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:39.189][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-06 16:02:39.206][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-06 16:02:39.222][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-12-06 16:02:39.231][biodb::testThat]
biodb.INFO [2025-12-06 16:02:39.233][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-06 16:02:39.236][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:39.238][biodb::testThat]
biodb.TRACE[2025-12-06 16:02:39.244][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-12-06 16:02:39.247][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:02:39.254][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-12-06 16:02:39.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:02:39.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:39.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:39.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:39.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:39.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:39.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-06 16:02:39.298][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.301][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.305][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.322][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.326][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.330][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.335][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.348][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.351][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.358][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.372][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.374][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.378][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.380][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.399][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.401][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.405][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.408][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.417][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.420][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.424][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.427][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.437][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-06 16:02:39.439][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.443][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.446][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-06 16:02:39.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.461][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:39.464][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:39.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.468][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:39.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:39.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.481][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:39.484][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:39.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.488][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:39.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:39.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.509][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:39.511][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:39.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.521][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:39.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:39.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.542][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:39.548][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:39.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.552][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.555][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:39.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:39.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.564][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-06 16:02:39.567][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:39.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.572][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-06 16:02:39.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:39.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.586][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:39.588][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:39.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.593][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:39.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:39.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.605][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:39.607][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:39.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.612][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.614][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:39.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:39.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.624][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-12-06 16:02:39.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.633][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.643][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:39.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.659][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-12-06 16:02:39.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.667][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:39.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.678][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-12-06 16:02:39.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.686][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.691][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:39.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.697][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-12-06 16:02:39.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.702][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.707][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:39.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.712][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-12-06 16:02:39.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.722][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:39.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:39.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:39.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.732][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.737][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.748][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:39.787][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-12-06 16:02:39.790][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:39.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:39.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.795][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:39.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:39.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.800][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:39.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:39.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.805][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:39.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:39.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.810][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:39.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:39.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.816][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:39.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:39.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:39.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:39.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.838][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.882][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.887][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.892][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:39.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.925][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.926][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.929][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:39.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:39.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.945][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-06 16:02:39.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.961][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-06 16:02:39.962][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.965][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.966][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-06 16:02:39.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:39.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-06 16:02:39.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:39.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:39.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:39.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:39.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:39.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:39.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:39.997][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-06 16:02:39.998][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:39.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.001][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-06 16:02:40.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:40.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:40.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:40.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:40.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:40.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:40.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.034][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:40.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:40.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.043][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.045][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:40.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:40.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.061][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:40.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:40.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.067][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:40.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:40.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.072][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:40.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:40.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.077][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:40.079][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:40.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.081][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.082][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:40.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:40.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.098][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.104][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.109][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.114][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.115][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.118][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.119][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.140][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.145][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.150][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.151][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.154][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.155][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.176][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.181][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.186][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.191][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.193][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.195][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.196][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.212][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.217][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.228][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.229][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.232][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.233][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.254][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.259][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.264][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.266][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.268][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.270][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.285][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.291][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.300][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.306][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.307][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.309][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.326][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.342][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.343][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.346][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.363][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:40.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:40.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:40.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:40.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:40.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:40.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.378][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:40.380][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:40.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.382][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:40.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:40.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.415][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.417][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.425][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.442][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:40.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:40.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.447][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:40.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:40.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:40.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:40.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.458][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:40.459][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:40.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.462][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.463][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:40.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:40.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.480][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.481][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.484][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.491][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.492][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.495][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.502][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.503][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.506][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.512][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.514][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.516][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.523][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.524][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.527][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.534][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.535][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.538][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.544][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:40.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:40.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.548][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.555][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:40.561][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:40.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.564][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.571][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.572][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.574][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.581][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:40.582][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:40.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.585][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.591][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:40.592][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:40.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.595][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.601][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:40.602][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:40.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.605][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.611][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:40.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:40.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.615][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.621][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.623][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.625][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.631][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.633][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.635][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.642][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-12-06 16:02:40.644][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:02:40.645][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-12-06 16:02:40.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:02:40.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:40.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:40.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:40.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:40.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:40.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-06 16:02:40.663][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.664][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.667][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.673][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.675][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.677][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.679][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.684][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.685][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.692][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.693][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.699][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.700][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.702][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.704][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.709][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.711][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.713][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.720][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.721][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.724][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.731][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-06 16:02:40.732][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:40.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.734][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.736][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-06 16:02:40.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:40.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.741][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:40.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:40.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.745][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:40.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:40.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.753][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:40.754][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:40.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.756][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:40.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:40.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.764][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.765][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.767][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.769][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:40.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.775][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:40.776][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:40.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.779][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.780][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:40.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:40.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.786][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-06 16:02:40.787][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:40.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.790][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-06 16:02:40.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:40.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.797][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.798][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.801][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.803][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:40.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.808][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.809][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.812][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.814][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:40.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.824][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-12-06 16:02:40.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.829][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.834][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:40.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.839][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-12-06 16:02:40.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.850][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:40.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.855][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-12-06 16:02:40.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.865][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:40.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.870][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-12-06 16:02:40.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.881][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:40.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.886][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-12-06 16:02:40.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.896][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:40.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:40.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:40.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.907][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:40.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:40.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.912][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:40.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:40.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.922][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:40.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:40.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:40.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:40.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:40.963][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-12-06 16:02:40.966][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:40.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:40.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.971][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:40.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:40.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.976][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:40.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:40.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.981][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:40.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.986][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:40.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:40.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.992][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:40.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:40.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:40.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:40.997][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:40.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:40.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.014][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:41.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:41.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.059][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:41.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:41.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.064][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:41.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:41.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.080][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:41.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:41.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.110][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.111][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.114][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.147][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.149][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.151][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.186][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.187][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.190][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:41.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:41.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:41.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:41.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:41.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.231][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:41.232][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:41.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.235][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.237][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:41.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:41.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.255][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:41.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.261][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:41.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.267][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:41.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:41.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.273][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:41.275][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:41.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.278][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.279][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:41.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:41.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.297][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.303][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.308][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.314][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.316][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.319][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.321][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.339][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.354][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.369][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.371][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.374][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.376][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.407][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.409][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.411][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:41.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:41.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:41.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:41.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:41.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:41.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.443][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:41.444][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:41.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.446][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.447][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:41.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:41.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.463][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.468][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.478][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.479][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.482][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.503][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.518][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.520][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.522][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.554][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.555][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.557][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.579][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.585][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.590][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.591][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.594][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.595][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.627][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.632][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.634][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.636][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.637][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:41.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:41.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:41.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:41.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:41.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:41.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.669][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:41.671][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:41.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.673][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:41.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.690][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:41.691][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:41.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.694][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.700][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.702][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-06 16:02:41.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.704][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.711][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.712][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-06 16:02:41.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.714][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.721][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.722][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-06 16:02:41.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.725][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.731][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.733][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-06 16:02:41.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.735][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.742][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.743][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-06 16:02:41.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.745][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.756][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-06 16:02:41.757][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-06 16:02:41.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.760][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.766][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-06 16:02:41.768][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-06 16:02:41.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.770][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.776][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.778][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-06 16:02:41.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.780][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.786][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-06 16:02:41.788][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-06 16:02:41.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.790][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.797][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.798][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:41.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.801][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.807][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.809][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-06 16:02:41.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.811][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.817][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:41.819][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:41.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.821][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.828][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.829][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-06 16:02:41.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.832][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:41.838][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.839][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-06 16:02:41.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.842][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:02:41.852][biodb::testThat]
biodb.INFO [2025-12-06 16:02:41.853][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-06 16:02:41.854][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:41.856][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:41.858][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-06 16:02:41.861][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-06 16:02:41.863][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:41.864][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:41.866][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:41.867][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:41.868][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:41.869][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:41.932][biodb::testThat]
biodb.INFO [2025-12-06 16:02:41.933][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-06 16:02:41.934][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:41.935][biodb::testThat]
biodb.TRACE[2025-12-06 16:02:41.939][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:41.941][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:41.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:41.943][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:41.945][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-12-06 16:02:41.956][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-06 16:02:41.958][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:41.960][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:41.961][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:41.963][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:41.964][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:41.965][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:41.967][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.030][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.031][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-06 16:02:42.032][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.034][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:42.043][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-06 16:02:42.045][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:42.047][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:42.048][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:42.049][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:42.051][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:42.052][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:42.053][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.117][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.118][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-06 16:02:42.119][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.121][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:42.126][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-06 16:02:42.127][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:42.129][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:42.130][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:42.131][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:42.133][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:42.134][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:42.135][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.195][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.196][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-06 16:02:42.197][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.198][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.263][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.264][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-06 16:02:42.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.266][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.325][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.327][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:42.332][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.334][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.394][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.395][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:42.397][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.398][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2025-12-06 16:02:42.472][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:42.474][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:42.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:42.476][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:42.477][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:42.479][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:42.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:42.481][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:02:42.483][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.485][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-12-06 16:02:42.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.487][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:42.496][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-06 16:02:42.498][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:42.500][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:42.501][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:42.502][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:42.504][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:42.505][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:42.506][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.571][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.572][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-12-06 16:02:42.573][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.575][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:42.578][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-06 16:02:42.580][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-06 16:02:42.582][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:42.583][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:42.584][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:42.586][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:42.587][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:42.588][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.648][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.650][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-12-06 16:02:42.651][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.652][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:42.656][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-06 16:02:42.658][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-06 16:02:42.659][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:42.661][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:42.667][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:42.669][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:42.670][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:42.671][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.732][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.733][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-12-06 16:02:42.734][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.736][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:42.739][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-06 16:02:42.741][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-06 16:02:42.743][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:42.744][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:42.746][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:42.747][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:42.748][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:42.749][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2025-12-06 16:02:42.811][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-06 16:02:42.812][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-06 16:02:42.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:42.815][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:42.816][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:42.817][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-06 16:02:42.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:42.819][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:02:42.821][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.823][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-12-06 16:02:42.824][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.825][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:42.828][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-06 16:02:42.830][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-06 16:02:42.832][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:42.833][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:42.834][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:42.835][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:42.837][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:42.838][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.900][biodb::testThat]
biodb.INFO [2025-12-06 16:02:42.901][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-12-06 16:02:42.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:42.904][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:42.907][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-06 16:02:42.909][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-06 16:02:42.910][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:42.912][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:42.913][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:42.914][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:42.915][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:42.917][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-06 16:02:42.973][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-06 16:02:42.975][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-12-06 16:02:42.976][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-06 16:02:42.977][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:42.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:42.979][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:42.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.119][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-06 16:02:43.125][biodb::testContext]
biodb.INFO [2025-12-06 16:02:43.126][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:43.127][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-12-06 16:02:43.128][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-06 16:02:43.130][biodb::testContext]
biodb.INFO [2025-12-06 16:02:43.132][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:43.134][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:43.138][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:43.140][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-06 16:02:43.141][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-06 16:02:43.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.145][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-06 16:02:43.147][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-06 16:02:43.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.151][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-06 16:02:43.152][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-06 16:02:43.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.157][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-06 16:02:43.158][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-06 16:02:43.159][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-06 16:02:43.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.163][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-06 16:02:43.165][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-06 16:02:43.166][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-06 16:02:43.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.170][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-06 16:02:43.171][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-06 16:02:43.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.176][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-06 16:02:43.177][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-06 16:02:43.178][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-06 16:02:43.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.183][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-06 16:02:43.184][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-06 16:02:43.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.188][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-06 16:02:43.190][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-06 16:02:43.191][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-06 16:02:43.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.195][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:43.196][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-06 16:02:43.198][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-06 16:02:43.199][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-06 16:02:43.200][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-06 16:02:43.201][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-06 16:02:43.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.206][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-06 16:02:43.207][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-06 16:02:43.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.211][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-06 16:02:43.213][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-06 16:02:43.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.217][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-06 16:02:43.218][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-06 16:02:43.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.223][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-06 16:02:43.224][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-06 16:02:43.225][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-06 16:02:43.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.229][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-06 16:02:43.231][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-06 16:02:43.241][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-06 16:02:43.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.245][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-06 16:02:43.247][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-06 16:02:43.248][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-06 16:02:43.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.252][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-06 16:02:43.255][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.256][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-06 16:02:43.257][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.258][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:43.260][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.261][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.262][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.263][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.265][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:43.266][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:43.267][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.268][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-06 16:02:43.270][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:43.271][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.272][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.273][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:43.273][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:43.273][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:43.273][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:43.273][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:43.275][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:43.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.279][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:43.281][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.282][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.284][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.285][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:43.288][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:43.289][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.291][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.293][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-06 16:02:43.295][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.297][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:43.298][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.300][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:43.301][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.304][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.306][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.307][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:43.309][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:43.310][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.312][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-06 16:02:43.313][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:43.315][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.316][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.318][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:43.318][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:43.318][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:43.318][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-06 16:02:43.318][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-06 16:02:43.319][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:43.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.323][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:43.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.329][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.330][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:43.331][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:43.332][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.334][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.335][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-06 16:02:43.338][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.340][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-06 16:02:43.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.343][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:43.344][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.346][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.347][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.349][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.350][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-06 16:02:43.352][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:43.353][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.355][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-06 16:02:43.356][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:43.358][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.359][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.361][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.362][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:43.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.366][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:43.368][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.369][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.371][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.372][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.374][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:43.375][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:43.376][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.378][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.380][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-06 16:02:43.382][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.384][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-06 16:02:43.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.387][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:43.388][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.390][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.391][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.393][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.394][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-06 16:02:43.396][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:43.397][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.399][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-06 16:02:43.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:43.402][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.403][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.405][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.406][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-06 16:02:43.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.411][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:43.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.415][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.416][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:43.419][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:43.421][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.422][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.424][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:43.425][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.536][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-06 16:02:43.539][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-06 16:02:43.541][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-06 16:02:43.543][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-06 16:02:43.545][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-06 16:02:43.547][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-06 16:02:43.549][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:43.551][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:43.553][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-06 16:02:43.555][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-06 16:02:43.557][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-06 16:02:43.559][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-06 16:02:43.561][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-06 16:02:43.563][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-06 16:02:43.565][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:43.568][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:43.570][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-06 16:02:43.572][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-06 16:02:43.574][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-06 16:02:43.576][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-06 16:02:43.578][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-06 16:02:43.580][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-06 16:02:43.582][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-06 16:02:43.584][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-06 16:02:43.586][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-06 16:02:43.588][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-06 16:02:43.590][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-06 16:02:43.592][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-06 16:02:43.594][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-06 16:02:43.596][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-06 16:02:43.603][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-06 16:02:43.604][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-06 16:02:43.606][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-06 16:02:43.608][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-06 16:02:43.609][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-06 16:02:43.611][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-06 16:02:43.613][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-06 16:02:43.614][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-06 16:02:43.616][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-06 16:02:43.618][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-06 16:02:43.619][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-06 16:02:43.621][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-06 16:02:43.623][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-06 16:02:43.624][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-06 16:02:43.626][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-06 16:02:43.628][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:43.629][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-06 16:02:43.631][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-06 16:02:43.633][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-06 16:02:43.634][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-06 16:02:43.636][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-06 16:02:43.638][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-06 16:02:43.639][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-06 16:02:43.641][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-06 16:02:43.643][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-06 16:02:43.645][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-06 16:02:43.646][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-06 16:02:43.648][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-06 16:02:43.650][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-06 16:02:43.652][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-06 16:02:43.654][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-06 16:02:43.656][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-06 16:02:43.657][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-06 16:02:43.659][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-06 16:02:43.661][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-06 16:02:43.662][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-06 16:02:43.664][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-06 16:02:43.666][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-06 16:02:43.668][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-06 16:02:43.669][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-06 16:02:43.671][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-06 16:02:43.673][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-06 16:02:43.675][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-06 16:02:43.676][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-06 16:02:43.678][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-06 16:02:43.680][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-06 16:02:43.681][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-06 16:02:43.683][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-06 16:02:43.685][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-06 16:02:43.686][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-06 16:02:43.688][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-06 16:02:43.690][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-06 16:02:43.692][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-06 16:02:43.693][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-06 16:02:43.695][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-06 16:02:43.696][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-06 16:02:43.697][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.700][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-06 16:02:43.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:43.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:43.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:43.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:43.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:43.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-06 16:02:43.828][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-06 16:02:43.830][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-06 16:02:43.832][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.834][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-06 16:02:43.835][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.836][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:43.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.839][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.840][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.841][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.842][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-06 16:02:43.844][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:43.845][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.846][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-06 16:02:43.847][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:43.849][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-06 16:02:43.849][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-06 16:02:43.850][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.851][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.853][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:43.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.856][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:43.857][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.860][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.861][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-06 16:02:43.861][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-06 16:02:43.862][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:43.863][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:43.865][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.866][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.868][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-06 16:02:43.870][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.872][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-06 16:02:43.873][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:43.875][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.877][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.878][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.879][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.880][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:43.882][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:43.883][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.884][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-06 16:02:43.885][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:43.887][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-06 16:02:43.887][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-06 16:02:43.887][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-06 16:02:43.887][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-06 16:02:43.887][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-06 16:02:43.887][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-06 16:02:43.888][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.889][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:43.891][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-06 16:02:43.892][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.893][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.894][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:43.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.897][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.898][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.899][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:43.899][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:43.900][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:43.901][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:43.903][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.904][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.906][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-06 16:02:43.908][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.909][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-06 16:02:43.911][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.912][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:43.913][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.914][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.916][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.917][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.918][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:43.919][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:43.921][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.922][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-06 16:02:43.923][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.924][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-06 16:02:43.926][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.927][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-06 16:02:43.927][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-06 16:02:43.927][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-06 16:02:43.929][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-06 16:02:43.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.932][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:43.934][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.936][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.937][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:43.937][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:43.937][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-06 16:02:43.938][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:43.940][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:43.941][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.942][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-06 16:02:43.944][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-06 16:02:43.946][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.947][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-06 16:02:43.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.950][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-06 16:02:43.951][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.952][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.954][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.955][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.956][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-06 16:02:43.958][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-06 16:02:43.959][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.960][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-06 16:02:43.961][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-06 16:02:43.963][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-06 16:02:43.963][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-06 16:02:43.964][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-06 16:02:43.965][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-06 16:02:43.967][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-06 16:02:43.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.970][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-06 16:02:43.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-06 16:02:43.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-06 16:02:43.974][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-06 16:02:43.975][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:43.975][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-06 16:02:43.975][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-06 16:02:43.976][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-06 16:02:43.977][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-06 16:02:43.979][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-06 16:02:43.980][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-06 16:02:43.982][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-06 16:02:43.983][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-06 16:02:43.985][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-06 16:02:43.987][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-06 16:02:43.989][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-06 16:02:43.991][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-06 16:02:43.998][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-06 16:02:44.007][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-12-06 16:02:44.012][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.013][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-06 16:02:44.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.016][biodb::testThat]
biodb.TRACE[2025-12-06 16:02:44.019][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-12-06 16:02:44.021][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-12-06 16:02:44.029][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-12-06 16:02:44.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-06 16:02:44.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:44.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:44.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:44.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:44.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:44.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-06 16:02:44.047][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.048][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.050][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.057][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.058][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.061][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.062][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.067][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.072][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.082][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-06 16:02:44.118][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-12-06 16:02:44.120][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:44.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:44.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.125][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-06 16:02:44.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-06 16:02:44.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.131][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:44.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-06 16:02:44.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.136][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:44.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:44.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.141][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-06 16:02:44.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-06 16:02:44.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.146][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:44.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-06 16:02:44.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.151][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:44.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-06 16:02:44.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.167][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.212][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.217][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.222][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-06 16:02:44.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.252][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.253][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.256][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.273][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.278][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.289][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.290][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.292][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.294][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.311][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-06 16:02:44.313][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-06 16:02:44.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.315][ef$get] fields variable is a list.
biodb.TRACE[2025-12-06 16:02:44.322][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.324][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-06 16:02:44.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-06 16:02:44.327][ef$get] fields variable is a list.
biodb.INFO [2025-12-06 16:02:44.338][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.339][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-06 16:02:44.340][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.342][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:44.345][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-12-06 16:02:44.348][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:44.350][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:44.352][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:44.353][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:44.354][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:44.356][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:44.357][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-06 16:02:44.416][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.417][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-06 16:02:44.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.419][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.427][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.429][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-06 16:02:44.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.431][biodb::testThat]
biodb.WARN [2025-12-06 16:02:44.435][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-06 16:02:44.441][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-06 16:02:44.452][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.454][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-06 16:02:44.455][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.456][biodb::testThat]
biodb.DEBUG[2025-12-06 16:02:44.461][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-12-06 16:02:44.463][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-12-06 16:02:44.465][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-06 16:02:44.466][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-12-06 16:02:44.467][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-06 16:02:44.469][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-06 16:02:44.470][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-06 16:02:44.471][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-06 16:02:44.535][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.537][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-06 16:02:44.538][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.539][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-06 16:02:44.600][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.601][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-06 16:02:44.603][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.604][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-06 16:02:44.665][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.666][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:44.667][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.669][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-06 16:02:44.729][biodb::testThat]
biodb.INFO [2025-12-06 16:02:44.730][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-06 16:02:44.731][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-06 16:02:44.733][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-06 16:02:44.791][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-06 16:02:44.792][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-12-06 16:02:44.793][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-06 16:02:44.794][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-06 16:02:44.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-06 16:02:44.797][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-06 16:02:44.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-06 16:02:44.799][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-06 16:02:44.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$getEntryPageUrl(id)
 12.                     └─private$doGetEntryPageUrl(entry.id)
 13.                       └─base::vapply(id, fct, FUN.VALUE = "")
 14.                         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$getEntryPageUrl(id)
 14.                         └─private$doGetEntryPageUrl(entry.id)
 15.                           └─base::vapply(id, fct, FUN.VALUE = "")
 16.                             └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 15.                           └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 16.                             └─self$getEntryPageUrl(id)
 17.                               └─private$doGetEntryPageUrl(entry.id)
 18.                                 └─base::vapply(id, fct, FUN.VALUE = "")
 19.                                   └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)

[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
Error:
! Test failures.
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
  Error:
  ! Test failures.
  Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log’
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)