Back to Long Tests report for BioC 3.22

This page was generated on 2025-09-20 23:55 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
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: 2025-09-20 09:55 -0400 (Sat, 20 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: 2025-09-20 16:01:07 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 16:02:10 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 63.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(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 [2025-09-20 16:02:06.358][biodb::testContext]
biodb.INFO [2025-09-20 16:02:06.359][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-20 16:02:06.360][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-20 16:02:06.361][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-20 16:02:06.362][biodb::testContext]
biodb.INFO [2025-09-20 16:02:06.368][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-09-20 16:02:06.369][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-20 16:02:06.376][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:02:06.377][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-20 16:02:06.378][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-20 16:02:06.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.381][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-20 16:02:06.397][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-20 16:02:06.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.401][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-20 16:02:06.402][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-20 16:02:06.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.405][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-20 16:02:06.406][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-20 16:02:06.407][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-20 16:02:06.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.410][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-20 16:02:06.411][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-20 16:02:06.412][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-20 16:02:06.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.416][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-20 16:02:06.417][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-20 16:02:06.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.419][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[2025-09-20 16:02:06.420][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-20 16:02:06.421][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-20 16:02:06.422][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-20 16:02:06.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.425][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-20 16:02:06.426][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-20 16:02:06.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.429][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-20 16:02:06.430][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-20 16:02:06.431][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-20 16:02:06.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.435][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-20 16:02:06.436][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-20 16:02:06.436][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-20 16:02:06.437][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-20 16:02:06.438][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-20 16:02:06.439][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-20 16:02:06.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.443][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-20 16:02:06.444][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-20 16:02:06.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.447][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-20 16:02:06.448][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-20 16:02:06.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.451][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-20 16:02:06.452][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-20 16:02:06.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.456][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-20 16:02:06.457][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-20 16:02:06.458][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-20 16:02:06.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.461][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-20 16:02:06.462][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-20 16:02:06.465][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-20 16:02:06.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.469][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-20 16:02:06.470][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-20 16:02:06.471][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-20 16:02:06.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.481][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-20 16:02:06.511][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.525][self$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[2025-09-20 16:02:06.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:02:06.528][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.529][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.531][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.532][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-20 16:02:06.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:02:06.533][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.534][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-20 16:02:06.535][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:02:06.536][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.537][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.538][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:02:06.538][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-20 16:02:06.538][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-20 16:02:06.538][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-20 16:02:06.538][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-20 16:02:06.539][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:02:06.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:06.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:06.542][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:02:06.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:06.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:06.544][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.545][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.546][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:02:06.547][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:02:06.548][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.549][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.550][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-20 16:02:06.551][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.552][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-20 16:02:06.553][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.554][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:02:06.555][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.556][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.557][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.558][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.559][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-20 16:02:06.559][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:02:06.560][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.561][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-20 16:02:06.562][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:02:06.563][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.564][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.565][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:02:06.565][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-20 16:02:06.565][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-20 16:02:06.565][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-20 16:02:06.565][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-20 16:02:06.566][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:02:06.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:06.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:06.569][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:02:06.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:06.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:06.571][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.572][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.573][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:02:06.574][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:02:06.575][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.576][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.577][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-20 16:02:06.578][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.579][self$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[2025-09-20 16:02:06.580][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.581][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:02:06.582][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.583][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.584][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.585][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.586][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-20 16:02:06.586][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:02:06.587][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.588][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-20 16:02:06.589][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:02:06.590][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.591][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.592][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.593][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:02:06.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:06.595][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:06.595][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:02:06.596][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:06.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:06.598][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.599][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.600][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:02:06.601][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:02:06.602][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.603][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.604][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-20 16:02:06.605][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.606][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-20 16:02:06.607][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.608][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:02:06.609][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.610][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.611][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.612][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.613][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-20 16:02:06.614][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:02:06.615][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.615][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-20 16:02:06.616][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:02:06.617][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.618][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.619][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.620][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-20 16:02:06.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:06.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:06.623][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:02:06.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:06.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:06.625][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.626][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.627][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:02:06.628][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:02:06.629][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.630][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:06.638][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:02:06.638][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.706][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-20 16:02:06.711][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-20 16:02:06.712][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-20 16:02:06.713][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-20 16:02:06.714][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-20 16:02:06.716][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-20 16:02:06.717][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-20 16:02:06.718][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-20 16:02:06.720][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-20 16:02:06.721][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-20 16:02:06.722][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-20 16:02:06.723][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-20 16:02:06.725][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-20 16:02:06.726][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-20 16:02:06.727][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-20 16:02:06.729][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-20 16:02:06.730][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-20 16:02:06.731][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-20 16:02:06.732][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-20 16:02:06.734][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-20 16:02:06.735][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-20 16:02:06.736][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-20 16:02:06.738][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-20 16:02:06.739][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-20 16:02:06.740][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-20 16:02:06.742][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-20 16:02:06.743][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-20 16:02:06.744][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-20 16:02:06.745][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-20 16:02:06.747][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-20 16:02:06.748][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-20 16:02:06.749][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-20 16:02:06.751][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-20 16:02:06.752][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-20 16:02:06.753][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-20 16:02:06.754][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-20 16:02:06.756][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-20 16:02:06.757][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-20 16:02:06.758][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-20 16:02:06.760][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-20 16:02:06.761][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-20 16:02:06.762][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-20 16:02:06.764][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-20 16:02:06.765][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-20 16:02:06.766][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-20 16:02:06.768][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-20 16:02:06.769][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-20 16:02:06.770][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-20 16:02:06.771][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-20 16:02:06.773][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-20 16:02:06.774][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-20 16:02:06.775][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-20 16:02:06.777][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-20 16:02:06.778][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-20 16:02:06.779][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-20 16:02:06.781][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-20 16:02:06.782][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-20 16:02:06.783][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-20 16:02:06.784][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-20 16:02:06.786][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-20 16:02:06.787][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-20 16:02:06.788][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-20 16:02:06.790][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-20 16:02:06.791][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-20 16:02:06.792][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-20 16:02:06.793][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-20 16:02:06.795][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-20 16:02:06.796][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-20 16:02:06.801][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-20 16:02:06.802][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-20 16:02:06.804][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-20 16:02:06.805][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-20 16:02:06.806][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-20 16:02:06.808][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-20 16:02:06.809][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-20 16:02:06.810][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-20 16:02:06.811][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-20 16:02:06.813][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-20 16:02:06.814][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-20 16:02:06.815][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-20 16:02:06.817][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-20 16:02:06.818][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-20 16:02:06.819][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-20 16:02:06.825][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-20 16:02:06.826][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-09-20 16:02:06.829][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-20 16:02:06.830][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.831][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.922][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[2025-09-20 16:02:06.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.928][FUN] Functions in observer BiodbConfig: [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 [2025-09-20 16:02:06.929][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-09-20 16:02:06.938][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-09-20 16:02:06.950][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-20 16:02:06.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-20 16:02:06.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:06.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:06.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:06.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:06.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:06.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-20 16:02:06.962][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-09-20 16:02:06.978][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-09-20 16:02:06.981][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.982][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.983][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.985][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-20 16:02:06.986][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.987][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-09-20 16:02:06.988][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-20 16:02:06.990][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-20 16:02:06.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-20 16:02:06.992][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:06.993][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-09-20 16:02:06.994][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-09-20 16:02:06.995][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-09-20 16:02:06.997][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-20 16:02:06.998][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-20 16:02:06.998][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-09-20 16:02:06.998][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-09-20 16:02:06.999][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-20 16:02:07.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:07.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:07.002][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-20 16:02:07.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-20 16:02:07.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-20 16:02:07.004][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-20 16:02:07.006][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-09-20 16:02:07.006][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-09-20 16:02:07.007][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-20 16:02:07.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-20 16:02:07.008][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-20 16:02:07.010][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-20 16:02:07.016][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-09-20 16:02:07.018][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-20 16:02:07.019][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-20 16:02:07.021][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-20 16:02:07.023][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-20 16:02:07.049][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-09-20 16:02:07.065][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-09-20 16:02:07.073][biodb::testThat]
biodb.INFO [2025-09-20 16:02:07.074][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-20 16:02:07.075][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:07.076][biodb::testThat]
biodb.TRACE[2025-09-20 16:02:07.080][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[2025-09-20 16:02:07.082][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-09-20 16:02:07.086][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-09-20 16:02:07.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-20 16:02:07.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:07.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:07.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:07.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:07.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:07.111][FUN] Functions in observer BiodbConfig: [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[2025-09-20 16:02:07.122][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.123][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.125][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.143][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.144][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.146][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.183][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.187][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.188][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.190][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.191][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.195][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.196][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.197][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.199][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.203][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.205][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.210][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.211][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.213][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.218][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.219][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.220][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.221][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.225][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.226][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.228][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.229][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.233][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.234][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.236][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.241][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.242][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.243][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.248][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.249][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.251][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.256][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:07.257][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:07.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.259][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:07.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:07.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.264][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.265][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.267][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.272][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.273][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.274][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.279][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.280][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.282][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.287][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.288][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.290][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.291][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.295][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:07.296][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:07.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.298][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.302][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:07.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:07.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.306][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-09-20 16:02:07.307][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:07.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.309][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.310][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-09-20 16:02:07.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:07.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.355][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.359][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.363][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.367][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.370][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.374][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:07.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.403][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.407][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:07.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.411][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.415][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:07.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.425][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:07.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:07.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:07.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:07.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.433][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:07.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:07.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.436][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.440][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.444][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.451][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:07.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:07.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:07.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:07.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:07.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:07.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.481][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.484][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.488][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:07.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.514][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.517][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.525][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.528][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.532][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.536][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:07.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:07.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.540][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:07.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:07.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.543][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:07.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:07.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.547][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-20 16:02:07.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.596][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-20 16:02:07.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:07.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.634][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.638][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.645][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:02:07.671][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-09-20 16:02:07.674][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:02:07.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:02:07.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-20 16:02:07.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-20 16:02:07.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.681][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-20 16:02:07.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-20 16:02:07.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.685][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-20 16:02:07.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-20 16:02:07.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.697][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.731][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.735][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.739][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-20 16:02:07.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.759][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.760][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.762][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:07.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:07.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.773][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.777][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.781][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.784][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.785][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.787][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.788][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:07.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.809][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.810][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.812][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:07.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.826][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.830][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.834][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.835][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.836][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.841][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:07.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.863][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.864][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.866][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:07.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.877][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.880][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.884][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.888][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.889][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.891][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.891][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:07.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.913][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.914][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.916][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:07.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:07.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.927][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.931][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.934][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.938][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.939][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.941][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.942][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:07.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:07.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.956][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.959][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.963][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.964][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.966][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.970][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:07.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:07.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.980][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.984][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.988][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.991][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.992][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.994][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:07.995][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:07.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:07.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.016][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.017][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.018][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.029][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.033][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.037][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.040][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.041][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.043][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.044][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.061][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.065][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.066][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.068][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.069][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.079][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.086][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.090][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.091][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.092][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.107][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:08.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:08.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.111][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:08.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:08.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.114][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:08.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:08.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.118][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:08.119][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:08.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.121][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.122][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:08.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:08.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:08.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:08.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:08.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:08.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.139][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:08.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:08.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.143][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:08.144][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:08.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.146][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:08.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:08.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.168][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.169][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.170][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.181][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.185][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.188][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.192][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.193][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.195][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.196][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.206][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-20 16:02:08.207][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-20 16:02:08.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.208][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.212][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-20 16:02:08.213][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-20 16:02:08.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.215][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.219][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.220][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-20 16:02:08.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.225][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-20 16:02:08.230][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-20 16:02:08.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.232][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.235][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:08.236][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-20 16:02:08.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.238][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.242][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.243][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-20 16:02:08.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.245][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.248][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.249][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-20 16:02:08.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.251][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.255][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.256][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-20 16:02:08.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.257][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.261][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:08.262][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:08.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.264][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.268][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-20 16:02:08.269][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-20 16:02:08.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.270][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.274][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-20 16:02:08.275][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-20 16:02:08.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.277][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.280][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.281][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-20 16:02:08.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.283][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.287][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:08.288][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-20 16:02:08.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.290][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.293][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.294][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-20 16:02:08.295][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.296][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.300][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:08.301][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:08.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.303][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.306][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:08.307][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-20 16:02:08.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.309][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.313][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:08.314][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:08.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.315][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.319][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-20 16:02:08.320][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-20 16:02:08.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.322][ef$get] fields variable is a list.
biodb.INFO [2025-09-20 16:02:08.328][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.329][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-20 16:02:08.330][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:08.331][biodb::testThat]
biodb.DEBUG[2025-09-20 16:02:08.347][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-20 16:02:08.349][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-20 16:02:08.352][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:02:08.379][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-20 16:02:08.380][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-20 16:02:08.381][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-20 16:02:08.416][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.417][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-20 16:02:08.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:08.419][biodb::testThat]
biodb.TRACE[2025-09-20 16:02:08.421][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:08.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:08.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.424][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-20 16:02:08.425][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-09-20 16:02:08.445][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-20 16:02:08.492][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-20 16:02:08.493][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:02:08.495][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-20 16:02:08.496][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-20 16:02:08.507][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-20 16:02:08.530][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.531][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-20 16:02:08.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:08.533][biodb::testThat]
biodb.DEBUG[2025-09-20 16:02:08.539][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-20 16:02:08.540][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-20 16:02:08.541][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:02:08.542][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-20 16:02:08.544][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-20 16:02:08.544][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-20 16:02:08.556][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.557][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-20 16:02:08.558][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:08.559][biodb::testThat]
biodb.DEBUG[2025-09-20 16:02:08.562][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-20 16:02:08.563][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-20 16:02:08.564][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-09-20 16:02:08.565][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-09-20 16:02:08.566][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-09-20 16:02:08.567][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-09-20 16:02:08.582][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.583][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-20 16:02:08.584][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:08.585][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.597][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.598][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-20 16:02:08.599][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:08.600][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.612][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.613][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-20 16:02:08.614][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:08.615][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.627][biodb::testThat]
biodb.INFO [2025-09-20 16:02:08.627][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-20 16:02:08.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-20 16:02:08.629][biodb::testThat]
biodb.TRACE[2025-09-20 16:02:08.653][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:08.654][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:08.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.656][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.657][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:08.658][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:08.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.660][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.661][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:08.662][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:08.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.663][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.664][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-20 16:02:08.665][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-20 16:02:08.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.667][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.668][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-20 16:02:08.669][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-20 16:02:08.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.671][ef$get] fields variable is a list.
biodb.TRACE[2025-09-20 16:02:08.672][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:08.673][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-20 16:02:08.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-20 16:02:08.675][ef$get] fields variable is a list.
biodb.INFO [2025-09-20 16:02:08.676][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-09-20 16:02:08.677][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-09-20 16:02:08.677][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-20 16:02:08.678][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-20 16:02:08.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-20 16:02:08.680][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-20 16:02:08.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-20 16:02:08.685][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-20 16:02:08.686][FUN] Functions in observer 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 Patched (2025-08-23 r88802)
* 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)