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 6/29HostnameOS / ArchCHECK
biodbHmdb 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-06 09:55 -0400 (Sat, 06 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: fa89c02
git_last_commit_date: 2025-07-24 10:45:35 -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 biodbHmdb on nebbiolo2

To the developers/maintainers of the biodbHmdb 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: biodbHmdb
Version: 1.15.1
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 biodbHmdb_1.15.1.tar.gz
StartedAt: 2025-09-06 16:01:18 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 16:02:20 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 62.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-09-06 16:02:17.879][biodb::testContext]
biodb.INFO [2025-09-06 16:02:17.881][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:02:17.882][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-06 16:02:17.883][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:02:17.884][biodb::testContext]
biodb.INFO [2025-09-06 16:02:17.890][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:02:17.891][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:02:17.898][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:02:17.899][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:02:17.900][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:02:17.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.903][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:02:17.920][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:02:17.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.923][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:02:17.924][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:02:17.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.928][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:02:17.928][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:02:17.929][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:02:17.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:17.933][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:02:17.934][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:02:17.935][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:02:17.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.938][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:02:17.939][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:02:17.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:17.942][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:02:17.943][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:02:17.944][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:02:17.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.947][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:02:17.948][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:02:17.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:17.952][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:02:17.953][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:02:17.954][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:02:17.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.957][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:02:17.958][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:02:17.959][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:02:17.960][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:02:17.961][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:02:17.962][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:02:17.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:17.965][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:02:17.966][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:02:17.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.969][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:02:17.970][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:02:17.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.974][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:02:17.975][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:02:17.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.978][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:02:17.979][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:02:17.980][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:02:17.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:17.983][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:02:17.984][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:02:17.988][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:02:17.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:17.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:17.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:17.991][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:02:17.992][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:02:17.993][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:02:17.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.004][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:02:18.036][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.050][self$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 16:02:18.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:18.053][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.054][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.055][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.056][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.057][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:02:18.058][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:18.059][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.060][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:02:18.061][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:18.061][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.062][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.063][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:02:18.063][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:02:18.063][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:02:18.063][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:02:18.063][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:02:18.064][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:02:18.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.067][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:18.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.070][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.071][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:18.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:18.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.074][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.075][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:02:18.077][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.078][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:02:18.078][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.079][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:18.080][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.081][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.082][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.083][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.084][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:02:18.085][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:18.086][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.087][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:02:18.088][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:18.089][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.089][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.090][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:02:18.090][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:02:18.090][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:02:18.090][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:02:18.090][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:02:18.091][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:02:18.092][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.094][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:18.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.096][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.097][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.098][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:18.099][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:18.100][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.101][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.102][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:02:18.104][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.104][self$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 16:02:18.105][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.106][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:18.107][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.108][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.109][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.110][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.111][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:02:18.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:18.113][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.114][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:02:18.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:18.116][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.116][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.117][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:02:18.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:18.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.124][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.124][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.125][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:18.126][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:18.127][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.128][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.129][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:02:18.131][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.132][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:02:18.133][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:18.134][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.135][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.136][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.137][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.138][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:02:18.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:18.140][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.141][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:02:18.142][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:18.143][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.144][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.144][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.145][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:02:18.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.148][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:18.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.151][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.151][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.152][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:18.153][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:18.154][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.155][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.163][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:02:18.164][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.167][FUN] 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 16:02:18.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.172][FUN] 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 16:02:18.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.176][FUN] 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 16:02:18.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.180][FUN] 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 16:02:18.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.184][FUN] 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 16:02:18.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.188][FUN] 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 16:02:18.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.192][FUN] 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 16:02:18.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.196][FUN] 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 16:02:18.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.200][FUN] 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 16:02:18.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.204][FUN] 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 16:02:18.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.209][FUN] 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 16:02:18.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.213][FUN] 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 16:02:18.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.217][FUN] 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 16:02:18.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.221][FUN] 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 16:02:18.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.225][FUN] 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 16:02:18.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.229][FUN] 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 16:02:18.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.232][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:02:18.236][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:02:18.237][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:02:18.239][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:02:18.240][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:02:18.241][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:02:18.242][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:02:18.244][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:02:18.245][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:02:18.246][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:02:18.248][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:02:18.249][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:02:18.250][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:02:18.251][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:02:18.253][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:02:18.254][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:02:18.255][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:02:18.256][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:02:18.258][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:02:18.259][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:02:18.260][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:02:18.262][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:02:18.263][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:02:18.264][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:02:18.265][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:02:18.267][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:02:18.268][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:02:18.269][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:02:18.271][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:02:18.272][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:02:18.273][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:02:18.274][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:02:18.276][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:02:18.277][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:02:18.278][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:02:18.279][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:02:18.281][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:02:18.282][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:02:18.283][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:02:18.285][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:02:18.286][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:02:18.287][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:02:18.288][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:02:18.290][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:02:18.291][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:02:18.292][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:02:18.294][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:02:18.295][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:02:18.296][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:02:18.297][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:02:18.299][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:02:18.300][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:02:18.301][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:02:18.303][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:02:18.304][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:02:18.305][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:02:18.306][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:02:18.308][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:02:18.309][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:02:18.310][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:02:18.312][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:02:18.313][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:02:18.314][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:02:18.315][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:02:18.317][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:02:18.318][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:02:18.319][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:02:18.321][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:02:18.326][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:02:18.327][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:02:18.329][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:02:18.330][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:02:18.331][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:02:18.333][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:02:18.334][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:02:18.335][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:02:18.336][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:02:18.338][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:02:18.339][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:02:18.340][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:02:18.342][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:02:18.343][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:02:18.344][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:02:18.350][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:02:18.351][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-06 16:02:18.354][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:02:18.355][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.356][FUN] 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 16:02:18.357][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.365][FUN] 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 16:02:18.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.371][FUN] 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 16:02:18.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:18.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.383][FUN] 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 16:02:18.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.389][FUN] 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 16:02:18.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.394][FUN] 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 16:02:18.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:18.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.406][FUN] 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 16:02:18.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.412][FUN] 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 16:02:18.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.417][FUN] 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 16:02:18.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:02:18.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:02:18.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.429][FUN] 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 16:02:18.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.443][FUN] 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 16:02:18.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.450][FUN] 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 16:02:18.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.457][FUN] 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 16:02:18.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:18.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.464][FUN] 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 16:02:18.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-09-06 16:02:18.468][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-09-06 16:02:18.480][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-09-06 16:02:18.496][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-06 16:02:18.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:02:18.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.514][FUN] 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 16:02:18.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.516][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 16:02:18.518][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-09-06 16:02:18.528][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-09-06 16:02:18.530][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.531][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.533][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.534][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:02:18.535][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.536][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-09-06 16:02:18.537][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.538][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.539][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:02:18.540][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:02:18.541][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.542][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-09-06 16:02:18.543][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-09-06 16:02:18.544][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-09-06 16:02:18.545][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:02:18.546][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:02:18.546][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-09-06 16:02:18.546][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-09-06 16:02:18.547][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:02:18.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.550][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:02:18.551][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:02:18.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:02:18.553][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:02:18.554][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-09-06 16:02:18.554][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-09-06 16:02:18.555][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:02:18.556][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:02:18.557][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:02:18.558][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:02:18.564][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-09-06 16:02:18.565][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:02:18.567][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:02:18.569][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:02:18.570][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:02:18.592][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-09-06 16:02:18.607][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-09-06 16:02:18.615][biodb::testThat]
biodb.INFO [2025-09-06 16:02:18.616][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-06 16:02:18.617][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:18.618][biodb::testThat]
biodb.TRACE[2025-09-06 16:02:18.622][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-09-06 16:02:18.624][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:02:18.627][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-09-06 16:02:18.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:02:18.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:18.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:18.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:18.651][FUN] 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 16:02:18.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:18.653][FUN] Functions in observer BiodbConfig: [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 16:02:18.664][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:18.665][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:18.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.667][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:18.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:18.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.683][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:18.684][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:18.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.686][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.718][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:18.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:18.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.722][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.723][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.725][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.726][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.730][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.731][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.733][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.734][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.738][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.739][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.740][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.745][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.746][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.748][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.753][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:18.754][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:18.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.756][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.757][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:18.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:18.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.761][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:18.762][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:18.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.763][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.764][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:18.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:18.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.768][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.769][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.771][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.772][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.776][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.777][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.779][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.780][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.783][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:18.784][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:18.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.786][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.787][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:18.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:18.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.791][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:18.792][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:18.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.794][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:18.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:18.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.799][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:18.800][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:18.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.801][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:18.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:18.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.806][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:18.807][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:18.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.809][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:18.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:18.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.814][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:18.815][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:18.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.817][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.818][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:18.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:18.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.821][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:18.822][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:18.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.824][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.825][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:18.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:18.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.829][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:18.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:18.831][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.832][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.836][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:18.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:18.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.840][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-09-06 16:02:18.841][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:18.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.843][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.844][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-09-06 16:02:18.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:18.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:18.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:18.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:18.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:18.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:18.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:18.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.889][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.893][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.897][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:18.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.901][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.904][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.908][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:18.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:18.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:18.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.938][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:18.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.945][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.952][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:18.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:18.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:18.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.963][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:18.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:18.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.967][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:18.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:18.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.970][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:18.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:18.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.974][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:18.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:18.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.978][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:18.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:18.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:18.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:18.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:18.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:18.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.989][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:18.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:18.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:18.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:18.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:18.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:18.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:18.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:18.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.000][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:19.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:19.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.014][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.018][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.022][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.040][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.047][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.051][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.055][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.059][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.062][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.066][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.070][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.073][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.077][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.081][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-06 16:02:19.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.129][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-06 16:02:19.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.168][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.171][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.179][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:19.204][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-09-06 16:02:19.207][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:02:19.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:02:19.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.210][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:02:19.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:02:19.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.214][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:02:19.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:02:19.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.218][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:02:19.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:02:19.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.230][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.264][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.267][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.271][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:02:19.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.291][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.292][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.294][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.305][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.309][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.313][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.316][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.317][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.319][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.320][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.341][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.342][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.344][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.354][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.358][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.362][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.365][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.366][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.368][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.373][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.394][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.395][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.396][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.407][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.411][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.414][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.418][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.419][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.421][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.422][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.442][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.443][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.445][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.456][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:19.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:19.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.460][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:19.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:19.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.463][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:19.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:19.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.467][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:19.468][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:19.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.470][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.471][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:19.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:19.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.481][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:19.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:19.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.484][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:19.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:19.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:19.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:19.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.492][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:19.493][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:19.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.495][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:19.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:19.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.509][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.517][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.520][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.521][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.522][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.523][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.524][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.545][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.546][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.548][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.570][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.571][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.573][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.574][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.584][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.587][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.591][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.595][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.596][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.597][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.598][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.609][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.620][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.621][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.622][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.623][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.637][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.641][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.644][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.648][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.649][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.651][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.652][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:19.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:19.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:19.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:19.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:19.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:19.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.673][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:19.674][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:19.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.676][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.677][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:19.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:19.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.698][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.699][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.699][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.700][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.701][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.711][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.715][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.718][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.722][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.723][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.725][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.726][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.736][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:02:19.737][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:02:19.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.738][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.742][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.743][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:02:19.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.745][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.749][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.750][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:02:19.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.755][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.759][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.760][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:02:19.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.762][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.765][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.766][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:02:19.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.768][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.772][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.773][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:02:19.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.775][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.778][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.779][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:02:19.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.781][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.785][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.786][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:02:19.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.788][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.791][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:19.792][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:19.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.794][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.798][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:02:19.799][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:02:19.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.800][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.804][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:02:19.805][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:02:19.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.807][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.811][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.812][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:02:19.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.813][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.817][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.818][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:02:19.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.820][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.823][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:02:19.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.826][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.830][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.831][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.833][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.836][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.837][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:02:19.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.839][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.843][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.844][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:19.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.846][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:19.849][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:02:19.850][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:02:19.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.852][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:02:19.858][biodb::testThat]
biodb.INFO [2025-09-06 16:02:19.859][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-06 16:02:19.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:19.861][biodb::testThat]
biodb.DEBUG[2025-09-06 16:02:19.877][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:02:19.881][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:02:19.883][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:19.910][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-06 16:02:19.912][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-06 16:02:19.912][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-06 16:02:19.947][biodb::testThat]
biodb.INFO [2025-09-06 16:02:19.948][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-06 16:02:19.949][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:19.949][biodb::testThat]
biodb.TRACE[2025-09-06 16:02:19.952][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:19.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:19.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:19.955][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:02:19.956][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-09-06 16:02:19.975][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:02:20.022][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:02:20.024][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:20.025][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-06 16:02:20.026][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-06 16:02:20.038][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-06 16:02:20.060][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.061][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-06 16:02:20.062][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:20.063][biodb::testThat]
biodb.DEBUG[2025-09-06 16:02:20.069][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:02:20.070][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:02:20.071][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:20.072][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-06 16:02:20.073][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-06 16:02:20.074][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-06 16:02:20.086][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.087][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-06 16:02:20.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:20.089][biodb::testThat]
biodb.DEBUG[2025-09-06 16:02:20.092][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:02:20.093][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:02:20.094][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-06 16:02:20.095][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-06 16:02:20.097][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-06 16:02:20.097][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-06 16:02:20.113][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.114][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-06 16:02:20.115][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:20.116][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.128][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.129][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-06 16:02:20.130][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:20.131][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.143][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.144][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-06 16:02:20.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:20.146][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.158][biodb::testThat]
biodb.INFO [2025-09-06 16:02:20.159][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-06 16:02:20.160][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:02:20.161][biodb::testThat]
biodb.TRACE[2025-09-06 16:02:20.186][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:20.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:20.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:20.189][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:20.190][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:20.191][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:20.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:20.192][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:20.193][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:20.194][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:20.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:20.196][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:20.197][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:02:20.198][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:02:20.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:20.200][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:20.201][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:02:20.202][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:02:20.202][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:20.203][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:02:20.204][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:20.205][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:02:20.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:02:20.207][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:02:20.208][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-06 16:02:20.209][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-09-06 16:02:20.210][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:02:20.211][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:02:20.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:02:20.212][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:02:20.217][FUN] 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 16:02:20.218][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:02:20.218][FUN] Functions in observer 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 8 | WARN 2 | SKIP 0 | PASS 103 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntry(id, drop = TRUE)
 4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
 5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 6.         └─conn$getEntryContent(ids)
 7.           └─self$download()
 8.             └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntry(id, drop = TRUE)
 4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
 5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 6.         └─conn$getEntryContent(ids)
 7.           └─self$download()
 8.             └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, 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$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can get a URL pointing to the entry page. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): We can get a URL pointing to the entry image. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): The entry page URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)

[ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
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 biodbHmdb_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.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 ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.15.1’
* 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 ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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:
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 0 | PASS 103 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.15.1’
** 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 EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
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 FileEntryMaker.cpp -o FileEntryMaker.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 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 StringEnrtryMaker.cpp -o StringEnrtryMaker.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 TagDetector.cpp -o TagDetector.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 XmlSplitter.cpp -o XmlSplitter.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 extractXmlEntries.cpp -o extractXmlEntries.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-TagDetector.cpp -o test-100-TagDetector.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-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.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-200-XmlSplitter.cpp -o test-200-XmlSplitter.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 biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' 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 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)