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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-08-16 16:01:10 -0400 (Sat, 16 Aug 2025)
EndedAt: 2025-08-16 16:02:11 -0400 (Sat, 16 Aug 2025)
EllapsedTime: 61.6 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-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-08-16 16:02:08.351][biodb::testContext]
biodb.INFO [2025-08-16 16:02:08.354][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:02:08.355][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-16 16:02:08.356][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:02:08.357][biodb::testContext]
biodb.INFO [2025-08-16 16:02:08.362][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:02:08.364][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-16 16:02:08.370][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:08.371][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-16 16:02:08.372][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-16 16:02:08.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.375][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-16 16:02:08.388][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-16 16:02:08.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.392][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-16 16:02:08.393][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-16 16:02:08.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.396][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-16 16:02:08.396][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-16 16:02:08.397][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-16 16:02:08.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.400][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-16 16:02:08.401][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-16 16:02:08.402][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-16 16:02:08.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.405][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-16 16:02:08.406][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-16 16:02:08.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.409][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-16 16:02:08.409][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-16 16:02:08.410][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-16 16:02:08.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.414][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-16 16:02:08.414][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-16 16:02:08.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.417][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-16 16:02:08.418][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-16 16:02:08.419][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-16 16:02:08.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.422][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:02:08.423][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-16 16:02:08.424][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-16 16:02:08.424][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-16 16:02:08.425][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-16 16:02:08.426][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-16 16:02:08.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.429][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-16 16:02:08.429][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-16 16:02:08.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.433][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-16 16:02:08.433][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-16 16:02:08.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.437][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-16 16:02:08.438][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-16 16:02:08.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.441][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-16 16:02:08.441][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-16 16:02:08.442][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-16 16:02:08.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.445][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:02:08.446][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-16 16:02:08.465][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-16 16:02:08.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:08.468][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-16 16:02:08.469][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-16 16:02:08.470][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-16 16:02:08.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.479][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-16 16:02:08.504][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.517][self$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 16:02:08.518][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:08.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.522][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.523][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:02:08.524][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:08.525][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.526][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-16 16:02:08.527][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:08.527][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.528][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.529][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:08.529][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:02:08.529][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:02:08.529][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:02:08.529][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:02:08.530][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:08.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.532][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:08.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.535][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.536][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.536][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:08.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:08.538][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.539][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.540][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-16 16:02:08.541][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.542][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:02:08.543][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.544][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:08.545][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.545][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.546][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.547][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.548][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:02:08.549][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:08.550][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.550][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-16 16:02:08.551][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:08.552][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.553][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.554][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:08.554][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:02:08.554][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:02:08.554][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:02:08.554][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:02:08.555][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:08.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.557][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:08.558][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.559][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.560][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.561][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.561][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:08.562][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:08.563][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.564][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.565][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-16 16:02:08.567][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.567][self$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 16:02:08.568][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.569][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:08.570][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.571][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.572][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.572][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.573][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:02:08.574][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:08.575][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.576][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-16 16:02:08.577][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:08.578][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.580][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.581][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:08.582][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.584][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:08.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.586][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.587][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.588][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:08.589][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:08.590][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.590][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.591][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-16 16:02:08.593][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.594][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:02:08.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.596][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:08.597][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.598][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.599][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.600][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.601][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:02:08.601][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:08.603][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.603][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-16 16:02:08.604][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:08.605][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.606][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.607][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.608][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:08.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.610][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:08.611][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.612][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.613][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.614][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:08.615][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:08.616][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.617][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.620][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:08.621][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.622][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 16:02:08.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.630][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 16:02:08.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.634][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 16:02:08.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.638][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 16:02:08.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.639][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 16:02:08.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.642][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 16:02:08.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.643][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 16:02:08.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.645][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 16:02:08.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:08.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.652][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 16:02:08.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.656][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 16:02:08.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:08.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.663][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 16:02:08.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.667][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 16:02:08.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.671][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 16:02:08.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.675][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 16:02:08.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.678][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 16:02:08.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.682][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 16:02:08.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.685][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 16:02:08.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.688][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-16 16:02:08.691][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-16 16:02:08.692][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-16 16:02:08.693][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-16 16:02:08.694][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-16 16:02:08.695][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:02:08.696][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-16 16:02:08.697][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-16 16:02:08.699][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-16 16:02:08.700][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:02:08.701][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:02:08.702][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-16 16:02:08.703][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-16 16:02:08.704][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-16 16:02:08.705][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-16 16:02:08.706][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:02:08.707][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-16 16:02:08.709][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-16 16:02:08.710][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-16 16:02:08.711][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-16 16:02:08.712][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-16 16:02:08.713][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-16 16:02:08.714][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-16 16:02:08.715][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-16 16:02:08.716][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-16 16:02:08.718][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-16 16:02:08.719][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-16 16:02:08.720][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-16 16:02:08.721][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-16 16:02:08.722][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-16 16:02:08.723][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-16 16:02:08.724][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-16 16:02:08.725][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-16 16:02:08.726][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-16 16:02:08.727][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-16 16:02:08.728][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-16 16:02:08.730][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-16 16:02:08.731][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-16 16:02:08.732][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-16 16:02:08.733][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-16 16:02:08.734][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-16 16:02:08.735][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-16 16:02:08.736][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-16 16:02:08.738][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-16 16:02:08.739][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-16 16:02:08.740][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-16 16:02:08.741][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-16 16:02:08.742][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-16 16:02:08.744][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-16 16:02:08.745][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-16 16:02:08.746][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-16 16:02:08.747][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-16 16:02:08.748][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-16 16:02:08.750][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-16 16:02:08.751][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-16 16:02:08.752][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-16 16:02:08.753][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-16 16:02:08.755][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-16 16:02:08.756][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-16 16:02:08.757][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-16 16:02:08.758][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-16 16:02:08.759][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-16 16:02:08.761][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-16 16:02:08.762][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-16 16:02:08.763][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-16 16:02:08.764][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-16 16:02:08.765][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-16 16:02:08.767][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-16 16:02:08.768][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-16 16:02:08.769][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-16 16:02:08.770][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-16 16:02:08.776][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-16 16:02:08.777][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-16 16:02:08.779][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-16 16:02:08.780][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-16 16:02:08.781][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-16 16:02:08.782][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-16 16:02:08.784][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-16 16:02:08.786][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-16 16:02:08.787][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-16 16:02:08.789][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-16 16:02:08.790][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-16 16:02:08.791][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-16 16:02:08.797][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-16 16:02:08.799][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:02:08.802][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:08.803][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.804][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 16:02:08.804][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.805][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 16:02:08.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.813][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 16:02:08.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.819][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 16:02:08.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.821][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 16:02:08.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.825][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 16:02:08.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.831][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 16:02:08.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.837][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 16:02:08.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.843][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 16:02:08.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.849][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 16:02:08.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.854][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 16:02:08.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.859][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 16:02:08.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.864][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 16:02:08.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.869][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 16:02:08.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.874][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 16:02:08.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.879][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 16:02:08.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:08.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.885][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 16:02:08.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.889][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 16:02:08.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:08.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:08.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:08.894][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 16:02:08.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:08.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:08.897][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-16 16:02:08.904][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-16 16:02:08.906][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.907][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-16 16:02:08.908][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.909][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:08.910][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.910][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-16 16:02:08.911][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.912][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.913][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-16 16:02:08.914][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:08.914][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.915][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-16 16:02:08.916][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:08.917][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-16 16:02:08.917][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-16 16:02:08.917][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-16 16:02:08.917][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-16 16:02:08.917][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-16 16:02:08.917][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-16 16:02:08.917][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-16 16:02:08.918][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:08.919][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.920][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-16 16:02:08.920][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.921][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.922][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:08.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:08.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:08.928][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:08.928][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:02:08.928][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:02:08.928][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-16 16:02:08.928][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-16 16:02:08.929][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:08.930][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:08.930][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:08.931][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:08.936][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-16 16:02:08.954][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-16 16:02:08.968][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-16 16:02:08.975][biodb::testThat]
biodb.INFO [2025-08-16 16:02:08.976][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-16 16:02:08.977][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:08.977][biodb::testThat]
biodb.TRACE[2025-08-16 16:02:08.980][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-08-16 16:02:08.981][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-16 16:02:08.984][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-16 16:02:08.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:02:08.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:08.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:09.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:09.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:09.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:09.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-16 16:02:09.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.070][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.089][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.093][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.099][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:02:09.146][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-08-16 16:02:09.148][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:02:09.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:02:09.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.152][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:02:09.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:02:09.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.158][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:02:09.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:02:09.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:02:09.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:02:09.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.188][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.239][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.243][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.246][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.266][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.267][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.268][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.280][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.289][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.290][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.292][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.293][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.312][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.313][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.315][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.336][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.337][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.338][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.364][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.365][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.378][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.379][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.380][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.385][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.386][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.387][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.392][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.393][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.394][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.398][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.399][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.401][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.405][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.406][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.407][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.421][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-08-16 16:02:09.448][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-08-16 16:02:09.450][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-08-16 16:02:09.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:02:09.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:09.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:09.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:09.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:09.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:09.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-16 16:02:09.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.519][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.526][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.560][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.579][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.582][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.589][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:02:09.615][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-08-16 16:02:09.631][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:02:09.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:02:09.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.635][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:02:09.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:02:09.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.638][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:02:09.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:02:09.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:02:09.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:02:09.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.652][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.679][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.683][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.686][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-08-16 16:02:09.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.716][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.717][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.718][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.730][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.733][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.737][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.740][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.741][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.742][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.743][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.762][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.765][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.776][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.785][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.786][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.787][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.809][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.809][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.811][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.837][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.838][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.840][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.865][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.866][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.868][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.882][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:09.883][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:09.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.884][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.890][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.891][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:09.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.892][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.900][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:09.902][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:09.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.904][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.910][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:09.912][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:09.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.915][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.922][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.924][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:09.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.926][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.934][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.935][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-16 16:02:09.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.937][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:09.942][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:09.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:09.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:09.945][ef$get] fields variable is a list.
biodb.INFO [2025-08-16 16:02:09.953][biodb::testThat]
biodb.INFO [2025-08-16 16:02:09.954][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-16 16:02:09.955][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:09.956][biodb::testThat]
biodb.DEBUG[2025-08-16 16:02:09.958][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-08-16 16:02:09.963][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-08-16 16:02:09.965][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:09.992][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-08-16 16:02:09.994][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-08-16 16:02:09.995][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-08-16 16:02:10.029][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.030][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-16 16:02:10.031][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:10.032][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.038][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.039][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-16 16:02:10.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:10.040][biodb::testThat]
biodb.WARN [2025-08-16 16:02:10.055][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-08-16 16:02:10.069][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-08-16 16:02:10.078][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.078][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-16 16:02:10.079][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:10.080][biodb::testThat]
biodb.DEBUG[2025-08-16 16:02:10.093][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-08-16 16:02:10.133][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:10.134][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:10.135][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-08-16 16:02:10.137][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-08-16 16:02:10.146][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-08-16 16:02:10.165][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.166][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-16 16:02:10.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:10.168][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.175][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.176][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-16 16:02:10.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:10.178][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.184][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.185][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-16 16:02:10.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:10.187][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.196][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.197][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-16 16:02:10.198][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:10.199][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.205][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-16 16:02:10.206][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-16 16:02:10.206][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-16 16:02:10.207][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.209][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.210][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-16 16:02:10.219][biodb::testContext]
biodb.INFO [2025-08-16 16:02:10.220][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:02:10.221][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-08-16 16:02:10.221][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:02:10.222][biodb::testContext]
biodb.INFO [2025-08-16 16:02:10.224][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:02:10.225][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-16 16:02:10.229][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:10.230][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-16 16:02:10.230][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.233][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-16 16:02:10.234][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.237][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-16 16:02:10.238][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.241][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-16 16:02:10.242][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-16 16:02:10.242][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-16 16:02:10.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.245][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-16 16:02:10.246][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-16 16:02:10.247][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.249][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-16 16:02:10.250][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-16 16:02:10.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.253][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-16 16:02:10.253][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-16 16:02:10.254][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-16 16:02:10.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.257][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-16 16:02:10.258][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.260][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-16 16:02:10.261][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-16 16:02:10.262][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.265][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:02:10.266][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-16 16:02:10.266][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-16 16:02:10.267][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-16 16:02:10.268][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-16 16:02:10.269][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-16 16:02:10.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.272][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-16 16:02:10.273][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-16 16:02:10.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.276][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-16 16:02:10.277][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-16 16:02:10.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.280][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-16 16:02:10.281][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-16 16:02:10.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.284][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-16 16:02:10.284][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-16 16:02:10.285][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-16 16:02:10.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.288][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:02:10.289][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-16 16:02:10.306][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-16 16:02:10.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.309][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-16 16:02:10.310][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-16 16:02:10.311][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-16 16:02:10.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.314][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-16 16:02:10.315][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.317][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-16 16:02:10.317][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.322][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.323][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.324][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.325][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.326][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.326][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:02:10.327][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.328][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.329][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-16 16:02:10.329][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.330][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.331][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.332][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:10.332][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:02:10.332][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:02:10.332][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:02:10.332][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:02:10.332][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:10.333][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.334][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.334][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.335][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.336][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.337][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.338][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.339][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.339][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.340][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.341][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-16 16:02:10.342][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.343][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:02:10.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.345][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.346][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.346][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.347][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.348][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.349][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:02:10.350][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.351][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.351][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-16 16:02:10.352][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.353][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.354][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.355][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:10.355][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:02:10.355][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:02:10.355][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:02:10.355][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:02:10.355][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:10.356][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.358][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.361][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.361][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.362][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.363][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.364][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.365][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-16 16:02:10.366][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.367][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-16 16:02:10.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.368][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.369][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.370][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.371][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.372][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:02:10.373][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.374][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.375][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-16 16:02:10.376][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.376][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.377][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.378][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.379][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:10.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.381][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.383][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.384][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.387][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.387][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.388][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-16 16:02:10.390][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.391][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:02:10.392][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.392][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.393][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.394][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.395][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.396][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.396][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:02:10.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.398][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.399][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-16 16:02:10.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.400][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.401][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.402][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.403][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:10.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.407][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.408][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.409][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.410][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.411][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.411][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.412][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:10.413][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.416][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 16:02:10.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.420][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 16:02:10.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.434][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 16:02:10.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.441][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 16:02:10.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.445][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 16:02:10.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.448][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 16:02:10.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.452][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 16:02:10.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.456][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 16:02:10.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.459][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 16:02:10.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.463][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 16:02:10.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.466][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 16:02:10.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.470][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 16:02:10.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.473][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 16:02:10.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.475][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-16 16:02:10.477][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-16 16:02:10.478][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-16 16:02:10.479][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-16 16:02:10.480][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-16 16:02:10.481][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:02:10.482][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-16 16:02:10.483][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-16 16:02:10.484][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-16 16:02:10.485][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:02:10.486][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:02:10.488][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-16 16:02:10.489][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-16 16:02:10.490][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-16 16:02:10.491][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-16 16:02:10.492][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:02:10.493][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-16 16:02:10.494][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-16 16:02:10.495][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-16 16:02:10.496][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-16 16:02:10.498][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-16 16:02:10.499][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-16 16:02:10.500][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-16 16:02:10.501][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-16 16:02:10.502][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-16 16:02:10.503][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-16 16:02:10.504][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-16 16:02:10.505][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-16 16:02:10.506][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-16 16:02:10.507][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-16 16:02:10.508][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-16 16:02:10.510][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-16 16:02:10.511][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-16 16:02:10.512][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-16 16:02:10.513][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-16 16:02:10.514][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-16 16:02:10.515][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-16 16:02:10.516][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-16 16:02:10.517][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-16 16:02:10.518][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-16 16:02:10.519][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-16 16:02:10.521][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-16 16:02:10.522][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-16 16:02:10.523][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-16 16:02:10.524][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-16 16:02:10.525][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-16 16:02:10.526][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-16 16:02:10.531][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-16 16:02:10.533][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-16 16:02:10.534][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-16 16:02:10.535][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-16 16:02:10.536][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-16 16:02:10.537][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-16 16:02:10.538][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-16 16:02:10.539][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-16 16:02:10.540][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-16 16:02:10.541][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-16 16:02:10.542][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-16 16:02:10.543][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-16 16:02:10.544][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-16 16:02:10.545][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-16 16:02:10.547][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-16 16:02:10.548][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-16 16:02:10.549][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-16 16:02:10.550][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-16 16:02:10.551][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-16 16:02:10.552][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-16 16:02:10.553][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-16 16:02:10.554][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-16 16:02:10.555][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-16 16:02:10.556][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-16 16:02:10.557][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-16 16:02:10.558][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-16 16:02:10.559][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-16 16:02:10.561][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-16 16:02:10.562][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-16 16:02:10.563][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-16 16:02:10.564][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-16 16:02:10.565][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-16 16:02:10.566][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-16 16:02:10.567][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-16 16:02:10.568][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-16 16:02:10.570][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-16 16:02:10.571][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-16 16:02:10.572][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:02:10.573][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:10.574][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.574][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 16:02:10.575][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.580][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 16:02:10.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.581][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 16:02:10.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.585][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 16:02:10.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.586][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 16:02:10.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.590][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 16:02:10.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.595][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 16:02:10.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.600][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 16:02:10.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.606][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 16:02:10.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.607][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 16:02:10.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.611][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 16:02:10.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.613][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 16:02:10.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.616][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 16:02:10.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.622][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 16:02:10.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.627][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 16:02:10.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.633][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 16:02:10.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.642][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 16:02:10.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.648][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 16:02:10.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.653][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 16:02:10.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.658][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 16:02:10.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.663][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 16:02:10.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:10.666][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-08-16 16:02:10.674][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-08-16 16:02:10.676][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.677][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-08-16 16:02:10.678][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.678][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.679][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.680][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-08-16 16:02:10.681][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.682][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.682][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-08-16 16:02:10.683][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.684][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.685][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-08-16 16:02:10.685][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.686][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-08-16 16:02:10.686][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-08-16 16:02:10.686][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-08-16 16:02:10.686][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-08-16 16:02:10.686][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-08-16 16:02:10.686][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-08-16 16:02:10.686][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-08-16 16:02:10.687][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.688][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.688][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-16 16:02:10.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.691][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.693][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.693][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:02:10.693][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-08-16 16:02:10.693][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-08-16 16:02:10.693][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-08-16 16:02:10.694][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.695][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.696][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.697][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.698][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-08-16 16:02:10.700][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-08-16 16:02:10.705][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-08-16 16:02:10.706][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-16 16:02:10.707][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-08-16 16:02:10.707][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-16 16:02:10.708][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.710][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.710][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 16:02:10.711][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.712][FUN] Functions in observer 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 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
  ‘/Users/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/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)