Back to Long Tests report for BioC 3.22

This page was generated on 2025-09-06 23:55 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
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: 2025-09-06 09:55 -0400 (Sat, 06 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 658b5cb
git_last_commit_date: 2025-07-24 10:46:27 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbNci on nebbiolo2

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

raw results


Summary

Package: biodbNci
Version: 1.13.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz
StartedAt: 2025-09-06 16:02:44 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 16:03:42 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 58.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-09-06 16:03:39.473][biodb::testContext]
biodb.INFO [2025-09-06 16:03:39.475][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:03:39.476][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-06 16:03:39.476][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:03:39.477][biodb::testContext]
biodb.INFO [2025-09-06 16:03:39.483][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:03:39.485][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:03:39.492][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:39.493][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:03:39.494][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:03:39.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.497][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:03:39.514][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:03:39.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.517][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:03:39.518][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:03:39.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.522][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:03:39.523][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:03:39.524][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:03:39.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.527][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:03:39.528][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:03:39.529][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:03:39.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.532][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:03:39.533][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:03:39.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.537][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:03:39.537][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:03:39.538][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:03:39.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.542][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:03:39.543][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:03:39.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.546][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:03:39.547][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:03:39.548][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:03:39.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.551][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:03:39.552][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:03:39.553][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:03:39.554][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:03:39.555][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:03:39.556][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:03:39.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.560][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:03:39.561][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:03:39.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.564][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:03:39.565][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:03:39.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.569][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:03:39.570][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:03:39.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.573][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:03:39.574][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:03:39.575][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:03:39.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.578][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:03:39.579][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:03:39.583][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:03:39.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.587][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:03:39.588][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:03:39.589][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:03:39.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.599][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:03:39.630][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.645][self$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[2025-09-06 16:03:39.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.647][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:39.647][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.648][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.649][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.650][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.651][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:03:39.652][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:39.653][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.654][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:03:39.655][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:39.656][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.657][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.658][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:03:39.658][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:03:39.658][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:03:39.658][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:03:39.658][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:03:39.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:39.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:39.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:39.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:39.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:39.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:39.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.665][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:39.666][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:39.667][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.668][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.669][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:03:39.671][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.672][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:03:39.673][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.674][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:39.675][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.676][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.676][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.677][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.678][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:03:39.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:39.680][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.681][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:03:39.682][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:39.683][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.684][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.685][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:03:39.685][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:03:39.685][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:03:39.685][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:03:39.685][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:03:39.686][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:39.687][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:39.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:39.688][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:39.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:39.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:39.691][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.692][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.693][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:39.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:39.694][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.695][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.696][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:03:39.698][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.699][self$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[2025-09-06 16:03:39.700][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.701][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:39.702][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.703][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.703][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.704][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.705][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:03:39.706][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:39.707][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.708][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:03:39.709][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:39.710][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.711][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.712][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.713][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:39.714][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:39.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:39.715][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:39.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:39.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:39.718][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.719][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.720][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:39.720][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:39.721][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.722][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.723][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:03:39.725][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.726][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:03:39.727][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.728][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:39.729][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.730][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.730][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.731][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.732][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:03:39.733][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:39.734][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.735][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:03:39.736][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:39.737][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.738][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:39.739][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.740][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:39.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:39.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:39.742][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:39.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:39.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:39.745][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:39.746][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.747][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:39.748][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:39.748][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:39.749][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:39.758][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:39.759][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.805][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[2025-09-06 16:03:39.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.827][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:03:39.831][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:03:39.833][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:03:39.834][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:03:39.835][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:03:39.837][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:03:39.838][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:03:39.839][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:03:39.841][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:03:39.842][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:03:39.843][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:03:39.845][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:03:39.846][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:03:39.847][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:03:39.849][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:03:39.850][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:03:39.852][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:03:39.853][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:03:39.854][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:03:39.855][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:03:39.857][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:03:39.858][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:03:39.859][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:03:39.861][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:03:39.862][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:03:39.863][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:03:39.864][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:03:39.866][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:03:39.867][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:03:39.868][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:03:39.870][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:03:39.871][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:03:39.872][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:03:39.873][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:03:39.875][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:03:39.876][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:03:39.877][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:03:39.878][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:03:39.880][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:03:39.881][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:03:39.882][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:03:39.884][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:03:39.885][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:03:39.886][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:03:39.887][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:03:39.889][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:03:39.890][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:03:39.891][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:03:39.893][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:03:39.894][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:03:39.895][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:03:39.896][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:03:39.898][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:03:39.899][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:03:39.900][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:03:39.902][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:03:39.903][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:03:39.904][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:03:39.905][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:03:39.907][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:03:39.908][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:03:39.909][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:03:39.911][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:03:39.912][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:03:39.913][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:03:39.914][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:03:39.916][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:03:39.917][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:03:39.922][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:03:39.924][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:03:39.925][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:03:39.926][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:03:39.927][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:03:39.929][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:03:39.930][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:03:39.931][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:03:39.933][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:03:39.934][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:03:39.935][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:03:39.936][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:03:39.938][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:03:39.939][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:03:39.940][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:03:39.946][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:03:39.947][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:03:39.950][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:39.951][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.953][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:39.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:39.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:39.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:39.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:39.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:39.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:39.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:39.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:39.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:39.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:39.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:39.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:39.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:39.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:39.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:39.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:39.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:39.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:39.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:40.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:40.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:40.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:40.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:40.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:40.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:40.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:40.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:40.063][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-09-06 16:03:40.074][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-09-06 16:03:40.077][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:40.078][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-09-06 16:03:40.079][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:40.080][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:40.081][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:40.082][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-09-06 16:03:40.083][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:40.084][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:40.085][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-09-06 16:03:40.086][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:40.087][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:40.088][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-09-06 16:03:40.089][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:40.091][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-09-06 16:03:40.091][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-09-06 16:03:40.091][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-09-06 16:03:40.091][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-09-06 16:03:40.091][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-09-06 16:03:40.091][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-09-06 16:03:40.091][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-09-06 16:03:40.092][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:40.107][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:40.108][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:03:40.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:40.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:40.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:40.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:40.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:40.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:40.115][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-06 16:03:40.115][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-06 16:03:40.115][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-09-06 16:03:40.115][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-09-06 16:03:40.116][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:40.117][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:40.118][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:40.119][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:40.126][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-09-06 16:03:40.148][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-09-06 16:03:40.164][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-09-06 16:03:40.173][biodb::testThat]
biodb.INFO [2025-09-06 16:03:40.174][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-06 16:03:40.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:40.176][biodb::testThat]
biodb.TRACE[2025-09-06 16:03:40.179][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-09-06 16:03:40.181][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:03:40.184][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-09-06 16:03:40.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:03:40.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:03:40.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.249][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.313][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.317][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.325][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:03:40.381][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-09-06 16:03:40.383][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:03:40.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:03:40.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.386][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:03:40.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:03:40.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.390][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:03:40.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:03:40.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.394][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:03:40.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:03:40.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.413][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.448][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.451][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.455][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.475][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.476][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.478][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.494][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.497][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.501][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.502][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.504][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.505][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.526][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.528][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.554][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.555][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.556][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.557][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.579][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.580][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.581][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.582][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.593][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.594][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.595][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.595][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.599][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.600][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.602][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.606][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.607][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.609][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.612][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.613][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.615][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.619][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.620][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.622][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.637][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-09-06 16:03:40.706][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:03:40.707][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-09-06 16:03:40.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:03:40.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:40.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:40.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:40.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:40.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:40.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-09-06 16:03:40.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.750][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.753][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.758][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:40.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:40.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:40.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:40.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:40.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.777][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:40.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:40.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:40.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:40.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:40.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:40.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:40.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:40.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:40.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:40.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:40.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:40.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:40.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:40.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:40.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.816][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.819][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.830][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:03:40.856][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-09-06 16:03:40.876][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:03:40.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:03:40.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.880][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:03:40.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:03:40.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.883][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:03:40.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:03:40.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.887][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:03:40.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:03:40.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.899][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.929][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.933][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.937][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-09-06 16:03:40.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.970][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.972][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:40.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:40.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.983][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.987][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.991][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.994][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.995][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:40.997][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:40.998][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:40.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:41.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:41.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:41.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:41.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:41.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:41.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:41.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.019][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:41.020][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:41.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.022][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:41.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:41.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:41.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:41.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.036][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:41.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:41.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:41.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:41.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.043][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:41.044][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:41.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.046][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:41.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:41.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.068][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.069][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.071][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:41.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:41.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:41.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:41.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:41.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:41.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.097][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:41.098][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:41.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.099][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:41.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:41.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.121][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.122][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.124][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.135][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:41.136][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:41.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.138][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.141][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:41.142][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:41.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.144][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.148][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:41.149][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:41.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.151][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.154][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:41.155][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:41.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.157][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.161][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.162][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:41.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.164][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.167][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.168][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-09-06 16:03:41.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.170][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:41.174][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:41.175][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:41.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:41.176][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:03:41.182][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.183][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-06 16:03:41.184][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:41.185][biodb::testThat]
biodb.DEBUG[2025-09-06 16:03:41.187][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-09-06 16:03:41.190][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-09-06 16:03:41.193][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-09-06 16:03:41.224][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-09-06 16:03:41.225][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-09-06 16:03:41.226][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-09-06 16:03:41.263][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.264][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-06 16:03:41.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:41.266][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.271][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.272][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-06 16:03:41.273][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:41.274][biodb::testThat]
biodb.WARN [2025-09-06 16:03:41.292][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-09-06 16:03:41.309][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-09-06 16:03:41.317][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.318][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-06 16:03:41.319][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:41.320][biodb::testThat]
biodb.DEBUG[2025-09-06 16:03:41.340][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2025-09-06 16:03:41.383][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:03:41.385][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-09-06 16:03:41.386][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-09-06 16:03:41.387][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-09-06 16:03:41.399][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.INFO [2025-09-06 16:03:41.421][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.422][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-06 16:03:41.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:41.423][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.433][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.434][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-06 16:03:41.435][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:41.436][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.442][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.443][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-06 16:03:41.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:41.444][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.449][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.450][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-06 16:03:41.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:41.452][biodb::testThat]
biodb.INFO [2025-09-06 16:03:41.457][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-06 16:03:41.458][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-09-06 16:03:41.459][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:03:41.460][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.461][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.463][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-09-06 16:03:41.472][biodb::testContext]
biodb.INFO [2025-09-06 16:03:41.473][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:03:41.474][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-09-06 16:03:41.475][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:03:41.476][biodb::testContext]
biodb.INFO [2025-09-06 16:03:41.478][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:03:41.479][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:03:41.483][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:41.484][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:03:41.485][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:03:41.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.488][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:03:41.504][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:03:41.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.507][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:03:41.508][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:03:41.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.512][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:03:41.513][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:03:41.514][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:03:41.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.517][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:03:41.518][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:03:41.519][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:03:41.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.522][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:03:41.523][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:03:41.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.527][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:03:41.528][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:03:41.528][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:03:41.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.532][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:03:41.533][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:03:41.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.536][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:03:41.537][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:03:41.538][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:03:41.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.541][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:03:41.542][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:03:41.543][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:03:41.544][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:03:41.549][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:03:41.550][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:03:41.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.553][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:03:41.554][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:03:41.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.558][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:03:41.559][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:03:41.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.562][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:03:41.563][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:03:41.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.566][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:03:41.567][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:03:41.568][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:03:41.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.572][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:03:41.572][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:03:41.576][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:03:41.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.580][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:03:41.581][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:03:41.582][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:03:41.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.585][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:03:41.587][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.588][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-06 16:03:41.589][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.590][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:41.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.591][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.592][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.593][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.594][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:03:41.595][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:41.596][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.597][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:03:41.598][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:41.599][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.600][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.601][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:03:41.601][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:03:41.601][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:03:41.601][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:03:41.601][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:03:41.602][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:41.603][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:41.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:41.604][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:41.605][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:41.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:41.607][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.608][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.609][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:41.609][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:41.610][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.611][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.612][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:03:41.614][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.615][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:03:41.616][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.617][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:41.618][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.619][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.620][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.620][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.621][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:03:41.622][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:41.623][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.624][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:03:41.625][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:41.626][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.627][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.628][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:03:41.628][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:03:41.628][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:03:41.628][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:03:41.628][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:03:41.629][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:41.630][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:41.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:41.631][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:41.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:41.633][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:41.634][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.635][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:41.637][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:41.637][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.638][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.640][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:03:41.641][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.642][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-06 16:03:41.643][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.644][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:41.645][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.646][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.647][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.649][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:03:41.650][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:41.650][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.651][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:03:41.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:41.653][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.654][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.655][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.656][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:41.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:41.658][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:41.659][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:41.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:41.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:41.661][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.662][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.663][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:41.664][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:41.665][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.666][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.667][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:03:41.672][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.673][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:03:41.674][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.675][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:41.676][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.677][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.678][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.678][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.679][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:03:41.680][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:41.681][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.682][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:03:41.683][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:41.684][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.685][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.686][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.687][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:41.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:41.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:41.689][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:41.690][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:41.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:41.692][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.693][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.694][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:41.695][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:41.695][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.696][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:41.698][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:41.698][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.712][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".
biodb.DEBUG[2025-09-06 16:03:41.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.766][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:03:41.768][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:03:41.769][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:03:41.770][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:03:41.771][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:03:41.773][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:03:41.774][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:03:41.775][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:03:41.777][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:03:41.778][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:03:41.779][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:03:41.781][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:03:41.782][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:03:41.783][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:03:41.784][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:03:41.786][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:03:41.790][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:03:41.792][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:03:41.793][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:03:41.794][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:03:41.796][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:03:41.797][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:03:41.798][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:03:41.799][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:03:41.801][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:03:41.802][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:03:41.803][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:03:41.805][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:03:41.806][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:03:41.807][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:03:41.808][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:03:41.810][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:03:41.811][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:03:41.812][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:03:41.814][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:03:41.815][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:03:41.816][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:03:41.817][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:03:41.819][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:03:41.820][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:03:41.821][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:03:41.823][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:03:41.824][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:03:41.825][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:03:41.827][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:03:41.828][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:03:41.829][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:03:41.830][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:03:41.832][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:03:41.833][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:03:41.834][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:03:41.836][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:03:41.837][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:03:41.838][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:03:41.839][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:03:41.841][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:03:41.842][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:03:41.843][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:03:41.845][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:03:41.846][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:03:41.847][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:03:41.848][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:03:41.850][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:03:41.851][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:03:41.852][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:03:41.854][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:03:41.855][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:03:41.856][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:03:41.857][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:03:41.859][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:03:41.860][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:03:41.861][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:03:41.863][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:03:41.864][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:03:41.865][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:03:41.866][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:03:41.868][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:03:41.869][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:03:41.870][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:03:41.872][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:03:41.873][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:03:41.874][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:03:41.875][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:03:41.881][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:03:41.882][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:03:41.883][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:41.884][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.886][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:41.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:41.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:41.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:41.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:41.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:41.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:41.985][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-09-06 16:03:41.986][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-09-06 16:03:41.988][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.989][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-09-06 16:03:41.990][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.991][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:41.992][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:41.993][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-09-06 16:03:41.994][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.994][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:41.995][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-09-06 16:03:41.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:41.997][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:41.998][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-09-06 16:03:41.999][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:42.000][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-09-06 16:03:42.000][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-09-06 16:03:42.000][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-09-06 16:03:42.000][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-09-06 16:03:42.000][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-09-06 16:03:42.000][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-09-06 16:03:42.000][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-09-06 16:03:42.001][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:42.002][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:42.003][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:03:42.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:42.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:42.006][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:42.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:42.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:42.008][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:42.009][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-06 16:03:42.009][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-09-06 16:03:42.009][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-09-06 16:03:42.009][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-09-06 16:03:42.010][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:42.011][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:42.012][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:42.013][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:42.014][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-09-06 16:03:42.017][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-09-06 16:03:42.020][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-09-06 16:03:42.021][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-06 16:03:42.022][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-09-06 16:03:42.023][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:03:42.028][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:42.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:42.029][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:42.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:42.031][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:42.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

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