Back to Long Tests report for BioC 3.22

This page was generated on 2025-08-16 23:55 -0400 (Sat, 16 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
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 8/29HostnameOS / ArchCHECK
biodbNci 1.13.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-16 09:55 -0400 (Sat, 16 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

To the developers/maintainers of the biodbNci 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: biodbNci
Version: 1.13.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-08-16 16:02:37 -0400 (Sat, 16 Aug 2025)
EndedAt: 2025-08-16 16:03:36 -0400 (Sat, 16 Aug 2025)
EllapsedTime: 59.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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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("biodbNci")
biodb.INFO [2025-08-16 16:03:32.545][biodb::testContext]
biodb.INFO [2025-08-16 16:03:32.547][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:03:32.548][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-16 16:03:32.549][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:03:32.550][biodb::testContext]
biodb.INFO [2025-08-16 16:03:32.556][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:03:32.557][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-16 16:03:32.564][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:03:32.565][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-16 16:03:32.566][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-16 16:03:32.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:32.569][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-16 16:03:32.586][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-16 16:03:32.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.588][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[2025-08-16 16:03:32.589][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-16 16:03:32.590][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-16 16:03:32.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:32.593][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-16 16:03:32.594][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-16 16:03:32.595][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-16 16:03:32.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.598][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[2025-08-16 16:03:32.599][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-16 16:03:32.600][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-16 16:03:32.601][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-16 16:03:32.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:32.604][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-16 16:03:32.605][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-16 16:03:32.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.607][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[2025-08-16 16:03:32.608][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-16 16:03:32.609][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-16 16:03:32.610][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-16 16:03:32.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:32.613][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-16 16:03:32.614][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-16 16:03:32.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.617][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[2025-08-16 16:03:32.618][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-16 16:03:32.619][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-16 16:03:32.619][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-16 16:03:32.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:32.623][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:03:32.624][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-16 16:03:32.625][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-16 16:03:32.626][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-16 16:03:32.627][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-16 16:03:32.628][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-16 16:03:32.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.630][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[2025-08-16 16:03:32.631][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-16 16:03:32.632][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-16 16:03:32.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:32.635][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-16 16:03:32.636][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-16 16:03:32.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.639][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[2025-08-16 16:03:32.639][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-16 16:03:32.640][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-16 16:03:32.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:32.644][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-16 16:03:32.645][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-16 16:03:32.646][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-16 16:03:32.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.648][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[2025-08-16 16:03:32.649][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:03:32.650][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-16 16:03:32.655][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-16 16:03:32.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:32.658][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-16 16:03:32.659][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-16 16:03:32.660][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-16 16:03:32.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.668][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[2025-08-16 16:03:32.671][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-16 16:03:32.702][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.716][self$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[2025-08-16 16:03:32.717][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.718][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:32.719][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.720][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.721][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.722][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.723][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:03:32.724][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:32.725][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.726][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-16 16:03:32.727][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:32.728][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.729][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.730][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:03:32.730][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:03:32.730][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:03:32.730][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:03:32.730][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:03:32.730][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:03:32.731][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:32.732][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:32.733][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:32.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:32.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:32.736][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.737][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.738][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:32.738][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:32.739][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.740][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.741][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-16 16:03:32.743][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.744][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:03:32.745][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.746][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:32.747][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.747][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.748][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.749][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.750][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:03:32.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:32.752][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.753][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-16 16:03:32.754][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:32.755][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.756][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.757][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:03:32.757][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:03:32.757][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:03:32.757][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:03:32.757][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:03:32.758][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:03:32.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:32.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:32.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:32.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:32.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:32.763][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.764][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.765][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:32.765][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:32.766][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.767][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.768][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-16 16:03:32.770][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.771][self$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[2025-08-16 16:03:32.772][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.773][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:32.774][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.775][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.776][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.776][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.777][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:03:32.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:32.779][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.780][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-16 16:03:32.781][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:32.782][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.783][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.784][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.785][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:03:32.786][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:32.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:32.787][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:32.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:32.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:32.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.791][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.792][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:32.793][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:32.793][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.794][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.795][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-16 16:03:32.797][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.798][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:03:32.799][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.800][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:32.801][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.802][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.803][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.804][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.804][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:03:32.805][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:32.806][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.807][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-16 16:03:32.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:32.809][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.810][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:32.811][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.812][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:03:32.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:32.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:32.814][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:32.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:32.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:32.817][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:32.818][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.819][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:32.820][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:32.820][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:32.821][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:32.830][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:03:32.831][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.831][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[2025-08-16 16:03:32.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.835][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[2025-08-16 16:03:32.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.840][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[2025-08-16 16:03:32.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.844][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[2025-08-16 16:03:32.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.848][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[2025-08-16 16:03:32.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.852][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[2025-08-16 16:03:32.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.856][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[2025-08-16 16:03:32.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.860][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[2025-08-16 16:03:32.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.864][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[2025-08-16 16:03:32.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.868][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[2025-08-16 16:03:32.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.872][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[2025-08-16 16:03:32.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.877][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[2025-08-16 16:03:32.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.881][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[2025-08-16 16:03:32.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.885][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[2025-08-16 16:03:32.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.889][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[2025-08-16 16:03:32.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.893][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[2025-08-16 16:03:32.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:32.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:32.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:32.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:32.897][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[2025-08-16 16:03:32.898][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-16 16:03:32.902][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-16 16:03:32.904][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-16 16:03:32.905][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-16 16:03:32.906][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-16 16:03:32.907][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:03:32.909][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-16 16:03:32.910][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-16 16:03:32.911][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-16 16:03:32.913][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:03:32.914][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:03:32.915][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-16 16:03:32.916][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-16 16:03:32.918][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-16 16:03:32.919][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-16 16:03:32.920][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:03:32.922][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-16 16:03:32.923][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-16 16:03:32.924][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-16 16:03:32.925][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-16 16:03:32.927][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-16 16:03:32.928][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-16 16:03:32.929][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-16 16:03:32.931][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-16 16:03:32.932][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-16 16:03:32.933][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-16 16:03:32.934][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-16 16:03:32.936][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-16 16:03:32.937][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-16 16:03:32.938][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-16 16:03:32.939][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-16 16:03:32.941][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-16 16:03:32.942][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-16 16:03:32.943][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-16 16:03:32.945][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-16 16:03:32.946][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-16 16:03:32.947][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-16 16:03:32.948][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-16 16:03:32.950][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-16 16:03:32.951][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-16 16:03:32.952][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-16 16:03:32.953][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-16 16:03:32.955][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-16 16:03:32.956][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-16 16:03:32.957][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-16 16:03:32.959][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-16 16:03:32.960][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-16 16:03:32.961][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-16 16:03:32.962][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-16 16:03:32.964][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-16 16:03:32.965][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-16 16:03:32.966][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-16 16:03:32.968][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-16 16:03:32.969][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-16 16:03:32.970][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-16 16:03:32.971][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-16 16:03:32.973][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-16 16:03:32.974][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-16 16:03:32.975][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-16 16:03:32.977][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-16 16:03:32.978][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-16 16:03:32.979][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-16 16:03:32.980][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-16 16:03:32.982][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-16 16:03:32.983][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-16 16:03:32.984][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-16 16:03:32.985][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-16 16:03:32.987][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-16 16:03:32.992][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-16 16:03:32.993][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-16 16:03:32.995][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-16 16:03:32.996][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-16 16:03:32.997][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-16 16:03:32.998][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-16 16:03:33.000][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-16 16:03:33.001][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-16 16:03:33.002][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-16 16:03:33.004][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-16 16:03:33.005][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-16 16:03:33.006][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-16 16:03:33.007][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-16 16:03:33.009][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-16 16:03:33.010][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-16 16:03:33.016][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-16 16:03:33.017][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:03:33.020][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:03:33.021][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.023][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.023][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[2025-08-16 16:03:33.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.033][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[2025-08-16 16:03:33.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.038][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[2025-08-16 16:03:33.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.044][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.DEBUG[2025-08-16 16:03:33.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.050][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[2025-08-16 16:03:33.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.056][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[2025-08-16 16:03:33.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.061][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[2025-08-16 16:03:33.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.067][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[2025-08-16 16:03:33.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.073][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[2025-08-16 16:03:33.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.078][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[2025-08-16 16:03:33.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.084][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[2025-08-16 16:03:33.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.099][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[2025-08-16 16:03:33.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.106][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[2025-08-16 16:03:33.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.113][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[2025-08-16 16:03:33.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.120][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.DEBUG[2025-08-16 16:03:33.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.126][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[2025-08-16 16:03:33.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:33.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.133][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[2025-08-16 16:03:33.135][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-16 16:03:33.147][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-16 16:03:33.150][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:33.151][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-16 16:03:33.152][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:33.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:33.154][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:33.155][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-16 16:03:33.156][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:33.157][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:33.158][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-16 16:03:33.159][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:33.160][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:33.161][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-16 16:03:33.162][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:33.163][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-16 16:03:33.163][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-16 16:03:33.163][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-16 16:03:33.163][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-16 16:03:33.163][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-16 16:03:33.163][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-16 16:03:33.163][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-16 16:03:33.164][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:33.180][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:33.181][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-16 16:03:33.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:33.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:33.184][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:33.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:33.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:33.187][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:33.188][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:03:33.188][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:03:33.188][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-16 16:03:33.188][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-16 16:03:33.189][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:33.190][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:33.191][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:33.192][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:33.199][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-16 16:03:33.221][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-16 16:03:33.238][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-16 16:03:33.247][biodb::testThat]
biodb.INFO [2025-08-16 16:03:33.248][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-16 16:03:33.249][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:33.250][biodb::testThat]
biodb.TRACE[2025-08-16 16:03:33.253][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-08-16 16:03:33.255][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-16 16:03:33.258][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-16 16:03:33.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:03:33.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-16 16:03:33.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.349][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.386][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.390][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.397][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:03:33.454][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-08-16 16:03:33.456][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:03:33.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:03:33.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:03:33.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:03:33.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.464][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:03:33.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:03:33.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.468][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:03:33.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:03:33.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.487][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.522][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.526][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.530][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.550][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.551][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.553][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.571][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.575][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.576][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.578][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.600][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.601][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.602][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.613][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.628][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.629][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.631][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.653][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.654][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.655][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.666][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.667][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.669][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.673][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.674][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.676][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.679][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.680][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.682][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.686][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.687][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.688][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.692][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.693][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.695][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.710][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-08-16 16:03:33.778][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-16 16:03:33.779][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-16 16:03:33.780][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:03:33.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:33.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:33.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:33.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:33.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:33.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-16 16:03:33.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.822][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:03:33.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:03:33.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.825][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:03:33.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:03:33.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.833][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:33.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:33.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:33.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:33.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:33.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:33.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:33.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:33.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:33.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:33.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:33.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:33.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:33.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:33.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:33.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:33.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:33.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:33.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:33.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:33.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.887][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.891][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.902][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:03:33.928][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-08-16 16:03:33.948][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:03:33.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:03:33.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.951][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:03:33.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:03:33.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.955][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:03:33.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:03:33.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.959][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:03:33.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:03:33.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.970][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:33.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:33.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:33.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:33.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:33.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.000][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:34.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:34.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.004][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:34.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:34.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.008][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:34.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:03:34.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:34.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:34.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:34.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:34.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:34.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:34.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.040][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:34.041][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:34.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.043][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:34.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:34.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.054][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.058][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.062][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.065][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.066][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.068][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.069][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:34.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:34.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:34.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:34.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:34.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:34.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.090][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:34.091][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:34.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.093][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:34.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:34.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:34.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:34.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.107][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:34.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:34.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:34.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:34.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.114][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:34.115][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:34.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.117][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:34.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:34.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.139][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.140][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.142][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:34.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:34.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:34.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:34.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:34.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:34.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.167][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:34.168][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:34.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.170][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:34.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:34.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.192][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.193][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.195][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.205][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:03:34.206][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:03:34.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.208][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.212][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.213][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:03:34.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.215][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.218][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:03:34.219][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:03:34.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.221][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.225][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:03:34.226][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:03:34.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.227][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.231][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.232][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:03:34.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.234][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.237][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.238][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:03:34.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.240][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:03:34.244][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:03:34.245][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:03:34.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:03:34.247][ef$get] fields variable is a list.
biodb.INFO [2025-08-16 16:03:34.253][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.254][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-16 16:03:34.255][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:34.255][biodb::testThat]
biodb.DEBUG[2025-08-16 16:03:34.257][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-08-16 16:03:34.260][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-08-16 16:03:34.263][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-08-16 16:03:34.294][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-08-16 16:03:34.295][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-08-16 16:03:34.296][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-08-16 16:03:34.333][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.334][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-16 16:03:34.335][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:34.336][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.341][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.342][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-16 16:03:34.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:34.344][biodb::testThat]
biodb.WARN [2025-08-16 16:03:34.361][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-08-16 16:03:34.379][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-08-16 16:03:34.386][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.387][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-16 16:03:34.388][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:34.389][biodb::testThat]
biodb.DEBUG[2025-08-16 16:03:34.410][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-08-16 16:03:34.453][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:03:34.455][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-08-16 16:03:34.456][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-08-16 16:03:34.457][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-08-16 16:03:34.469][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-08-16 16:03:34.491][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.492][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-16 16:03:34.493][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:34.494][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.503][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.504][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-16 16:03:34.505][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:34.506][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.512][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.513][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-16 16:03:34.514][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:34.515][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.520][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.521][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-16 16:03:34.522][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:03:34.523][biodb::testThat]
biodb.INFO [2025-08-16 16:03:34.527][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-16 16:03:34.528][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-16 16:03:34.529][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-16 16:03:34.530][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.532][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.533][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-16 16:03:34.543][biodb::testContext]
biodb.INFO [2025-08-16 16:03:34.544][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:03:34.545][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-08-16 16:03:34.546][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:03:34.546][biodb::testContext]
biodb.INFO [2025-08-16 16:03:34.548][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:03:34.550][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-16 16:03:34.553][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:03:34.554][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-16 16:03:34.555][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-16 16:03:34.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.558][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[2025-08-16 16:03:34.559][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-16 16:03:34.560][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-16 16:03:34.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:34.563][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-16 16:03:34.564][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-16 16:03:34.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.566][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[2025-08-16 16:03:34.567][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-16 16:03:34.568][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-16 16:03:34.569][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-16 16:03:34.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:34.573][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-16 16:03:34.573][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-16 16:03:34.574][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-16 16:03:34.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.577][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[2025-08-16 16:03:34.578][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-16 16:03:34.579][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-16 16:03:34.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:34.582][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-16 16:03:34.583][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-16 16:03:34.584][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-16 16:03:34.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.586][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[2025-08-16 16:03:34.587][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-16 16:03:34.588][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-16 16:03:34.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:34.592][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-16 16:03:34.593][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-16 16:03:34.593][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-16 16:03:34.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.596][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[2025-08-16 16:03:34.597][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:03:34.598][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-16 16:03:34.599][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-16 16:03:34.600][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-16 16:03:34.601][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-16 16:03:34.601][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-16 16:03:34.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:34.605][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-16 16:03:34.606][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-16 16:03:34.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.608][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[2025-08-16 16:03:34.609][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-16 16:03:34.610][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-16 16:03:34.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:34.614][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-16 16:03:34.615][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-16 16:03:34.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.617][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[2025-08-16 16:03:34.618][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-16 16:03:34.619][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-16 16:03:34.624][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-16 16:03:34.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:34.627][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:03:34.628][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-16 16:03:34.632][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-16 16:03:34.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.635][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[2025-08-16 16:03:34.635][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-16 16:03:34.636][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-16 16:03:34.637][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-16 16:03:34.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:03:34.641][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-16 16:03:34.642][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.643][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-16 16:03:34.644][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.645][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:34.646][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.647][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.648][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.649][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.650][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:03:34.651][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:34.652][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.653][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-16 16:03:34.654][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:34.655][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.656][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.656][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:03:34.656][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:03:34.656][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:03:34.656][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:03:34.656][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:03:34.657][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:03:34.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:34.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:34.660][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:34.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:34.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:34.663][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.664][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.665][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:34.665][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:34.666][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.667][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.668][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-16 16:03:34.670][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.671][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:03:34.672][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.673][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:34.674][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.675][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.675][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.676][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.677][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:03:34.678][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:34.679][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.680][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-16 16:03:34.681][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:34.682][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.683][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.684][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:03:34.684][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:03:34.684][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:03:34.684][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:03:34.684][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:03:34.685][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:03:34.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:34.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:34.687][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:34.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:34.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:34.690][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.691][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:34.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:34.693][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.694][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.695][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-16 16:03:34.697][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.698][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-16 16:03:34.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:34.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.703][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.703][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.704][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:03:34.705][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:34.706][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.707][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-16 16:03:34.708][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:34.709][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.710][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.711][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:03:34.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:34.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:34.714][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:34.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:34.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:34.717][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.718][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.719][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:34.720][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:34.721][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.721][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.723][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-16 16:03:34.724][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.725][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:03:34.726][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.727][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:34.728][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.729][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.730][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.731][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.732][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:03:34.732][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:34.733][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.734][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-16 16:03:34.735][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:34.736][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.737][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:34.738][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.739][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:03:34.740][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:34.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:34.742][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:34.742][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:34.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:34.748][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:34.749][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.750][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:34.750][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:34.751][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:34.752][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:34.753][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:03:34.754][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.755][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[2025-08-16 16:03:34.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.759][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[2025-08-16 16:03:34.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.763][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[2025-08-16 16:03:34.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.768][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[2025-08-16 16:03:34.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.772][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[2025-08-16 16:03:34.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.776][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[2025-08-16 16:03:34.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.780][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[2025-08-16 16:03:34.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.784][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[2025-08-16 16:03:34.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.788][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[2025-08-16 16:03:34.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.792][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[2025-08-16 16:03:34.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.797][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[2025-08-16 16:03:34.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.801][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[2025-08-16 16:03:34.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.805][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[2025-08-16 16:03:34.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.809][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[2025-08-16 16:03:34.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.813][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[2025-08-16 16:03:34.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.817][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[2025-08-16 16:03:34.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.821][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[2025-08-16 16:03:34.822][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-16 16:03:34.823][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-16 16:03:34.825][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-16 16:03:34.826][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-16 16:03:34.827][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-16 16:03:34.829][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:03:34.830][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-16 16:03:34.831][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-16 16:03:34.832][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-16 16:03:34.834][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:03:34.835][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:03:34.836][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-16 16:03:34.838][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-16 16:03:34.839][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-16 16:03:34.840][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-16 16:03:34.841][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:03:34.843][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-16 16:03:34.844][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-16 16:03:34.845][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-16 16:03:34.847][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-16 16:03:34.848][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-16 16:03:34.849][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-16 16:03:34.851][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-16 16:03:34.852][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-16 16:03:34.853][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-16 16:03:34.854][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-16 16:03:34.856][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-16 16:03:34.857][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-16 16:03:34.858][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-16 16:03:34.860][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-16 16:03:34.861][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-16 16:03:34.866][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-16 16:03:34.867][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-16 16:03:34.868][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-16 16:03:34.870][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-16 16:03:34.871][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-16 16:03:34.872][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-16 16:03:34.873][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-16 16:03:34.875][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-16 16:03:34.876][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-16 16:03:34.877][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-16 16:03:34.879][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-16 16:03:34.880][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-16 16:03:34.881][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-16 16:03:34.882][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-16 16:03:34.884][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-16 16:03:34.885][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-16 16:03:34.886][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-16 16:03:34.888][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-16 16:03:34.889][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-16 16:03:34.890][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-16 16:03:34.892][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-16 16:03:34.893][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-16 16:03:34.894][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-16 16:03:34.895][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-16 16:03:34.897][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-16 16:03:34.898][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-16 16:03:34.899][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-16 16:03:34.901][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-16 16:03:34.902][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-16 16:03:34.903][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-16 16:03:34.904][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-16 16:03:34.906][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-16 16:03:34.907][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-16 16:03:34.908][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-16 16:03:34.910][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-16 16:03:34.911][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-16 16:03:34.912][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-16 16:03:34.913][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-16 16:03:34.915][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-16 16:03:34.916][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-16 16:03:34.917][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-16 16:03:34.919][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-16 16:03:34.920][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-16 16:03:34.921][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-16 16:03:34.922][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-16 16:03:34.924][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-16 16:03:34.925][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-16 16:03:34.926][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-16 16:03:34.927][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-16 16:03:34.929][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-16 16:03:34.930][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-16 16:03:34.931][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-16 16:03:34.933][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-16 16:03:34.934][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:03:34.935][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:03:34.936][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.938][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.938][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[2025-08-16 16:03:34.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.944][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[2025-08-16 16:03:34.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.950][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[2025-08-16 16:03:34.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.956][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[2025-08-16 16:03:34.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.961][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[2025-08-16 16:03:34.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.967][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[2025-08-16 16:03:34.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.973][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[2025-08-16 16:03:34.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.979][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[2025-08-16 16:03:34.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.989][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[2025-08-16 16:03:34.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:34.994][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[2025-08-16 16:03:34.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:34.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:34.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:34.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:34.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:34.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:35.000][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[2025-08-16 16:03:35.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:35.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:35.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:35.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:35.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:35.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:35.006][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[2025-08-16 16:03:35.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:35.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:35.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:35.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:35.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:35.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:35.012][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[2025-08-16 16:03:35.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:35.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:35.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:35.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:35.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:35.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:35.017][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[2025-08-16 16:03:35.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:35.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:35.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:35.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:35.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:35.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:35.023][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[2025-08-16 16:03:35.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:35.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:35.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:35.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:35.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:35.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:35.029][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[2025-08-16 16:03:35.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:03:35.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:35.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:35.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:35.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:35.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:35.035][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[2025-08-16 16:03:35.036][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-16 16:03:35.037][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-16 16:03:35.039][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:35.040][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-16 16:03:35.041][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:35.042][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:03:35.043][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:35.044][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-16 16:03:35.045][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:35.046][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:03:35.047][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-16 16:03:35.048][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:03:35.049][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:35.049][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-16 16:03:35.050][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:03:35.051][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-16 16:03:35.051][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-16 16:03:35.051][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-16 16:03:35.051][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-16 16:03:35.051][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-16 16:03:35.051][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-16 16:03:35.051][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-16 16:03:35.052][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-16 16:03:35.053][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:35.054][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-16 16:03:35.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:35.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:35.057][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:03:35.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:03:35.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:03:35.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:03:35.060][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:03:35.060][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:03:35.060][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-16 16:03:35.060][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-16 16:03:35.061][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:03:35.062][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:03:35.063][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-16 16:03:35.064][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:03:35.065][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-16 16:03:35.068][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-16 16:03:35.072][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-16 16:03:35.073][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-16 16:03:35.074][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-16 16:03:35.074][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-16 16:03:35.075][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:03:35.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:03:35.077][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:03:35.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:03:35.078][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:03:35.079][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 2 | WARN 0 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, 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$getEntryContent(ids)
 8.             └─self$download()
 9.               └─private$doExtractDownload()

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.13.1’
* 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 ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... 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:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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 = `<NcCctsCn>`, 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$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.13.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** 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 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)