Back to Long Tests report for BioC 3.22

This page was generated on 2026-01-31 23:55 -0500 (Sat, 31 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4888
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4678
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 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-01-31 09:55 -0500 (Sat, 31 Jan 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2026-01-31 16:01:08 -0500 (Sat, 31 Jan 2026)
EndedAt: 2026-01-31 16:02:16 -0500 (Sat, 31 Jan 2026)
EllapsedTime: 68.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2026-01-31 16:02:13.440][biodb::testContext]
biodb.INFO [2026-01-31 16:02:13.442][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:13.443][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-01-31 16:02:13.444][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:13.444][biodb::testContext]
biodb.INFO [2026-01-31 16:02:13.450][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:13.452][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:13.458][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:13.459][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:02:13.460][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:02:13.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.464][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:02:13.480][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:02:13.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.483][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:02:13.484][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:02:13.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.487][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:02:13.488][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:02:13.489][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:02:13.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.493][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:02:13.494][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:02:13.495][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:02:13.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.498][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:02:13.499][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:02:13.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.502][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:02:13.503][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:02:13.504][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:02:13.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.508][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:02:13.509][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:02:13.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.512][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:02:13.513][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:02:13.514][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:02:13.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.517][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:13.518][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:02:13.519][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:02:13.520][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:02:13.521][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:02:13.522][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:02:13.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.525][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:02:13.526][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:02:13.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.530][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:02:13.531][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:02:13.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.534][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:02:13.535][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:02:13.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.538][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:02:13.539][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:02:13.540][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:02:13.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.544][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:13.545][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:02:13.548][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:02:13.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.552][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:02:13.553][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:02:13.554][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:02:13.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.559][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:02:13.590][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.610][self$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[2026-01-31 16:02:13.611][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.612][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:13.613][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.614][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.616][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:13.617][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:13.618][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.619][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:02:13.620][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:13.621][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.622][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.623][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:13.623][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:13.623][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:13.623][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:13.623][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:13.624][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:13.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:13.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:13.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:13.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:13.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:13.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.630][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.631][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:13.632][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:13.632][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.633][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.634][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:02:13.636][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.637][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:13.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.639][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:13.640][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.641][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.642][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.643][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.643][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:13.644][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:13.645][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.646][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:02:13.647][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:13.648][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.649][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.650][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:13.650][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:13.650][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:13.650][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:13.650][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:13.651][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:13.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:13.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:13.654][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:13.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:13.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:13.656][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.657][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.658][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:13.659][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:13.660][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.661][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.662][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:02:13.663][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.664][self$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[2026-01-31 16:02:13.665][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:13.667][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.669][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.671][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:13.672][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:13.673][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.674][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:02:13.675][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:13.675][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.676][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.677][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.678][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:13.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:13.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:13.681][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:13.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:13.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:13.683][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.684][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.685][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:13.686][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:13.687][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.688][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.689][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:02:13.691][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.692][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:13.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:13.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.696][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.697][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.698][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:13.699][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:13.700][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.701][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:02:13.702][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:13.703][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.704][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:13.705][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.706][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:13.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:13.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:13.708][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:13.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:13.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:13.711][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:13.712][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:13.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:13.714][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:13.715][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:13.719][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:13.720][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.799][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:02:13.804][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:02:13.806][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:02:13.807][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:02:13.809][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:02:13.810][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:13.812][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:13.813][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:13.815][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:02:13.816][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:13.835][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:13.837][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:02:13.838][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:13.839][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:13.841][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:13.842][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:13.844][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:02:13.845][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:02:13.847][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:02:13.848][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:02:13.850][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:02:13.851][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:02:13.853][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:02:13.854][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:02:13.855][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:02:13.857][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:02:13.858][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:02:13.860][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:02:13.861][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:02:13.863][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:02:13.864][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:02:13.865][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:02:13.867][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:02:13.868][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:02:13.870][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:02:13.871][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:02:13.872][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:02:13.874][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:02:13.875][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:02:13.877][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:02:13.878][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:02:13.879][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:02:13.881][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:02:13.882][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:02:13.884][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:02:13.885][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:13.887][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:02:13.888][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:02:13.889][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:02:13.891][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:02:13.892][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:02:13.894][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:02:13.895][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:02:13.896][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:02:13.898][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:02:13.899][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:02:13.901][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:02:13.902][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:02:13.904][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:02:13.905][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:02:13.906][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:02:13.908][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:02:13.909][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:02:13.911][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:02:13.912][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:02:13.913][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:02:13.915][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:02:13.916][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:02:13.918][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:02:13.919][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:02:13.920][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:02:13.922][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:02:13.923][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:02:13.925][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:02:13.926][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:02:13.927][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:02:13.929][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:02:13.930][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:02:13.932][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:02:13.933][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:02:13.934][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:02:13.936][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:02:13.937][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:02:13.944][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:02:13.946][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:13.949][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:13.950][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.952][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:13.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:13.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:13.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:13.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:13.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:13.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:13.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:13.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:13.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:13.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:13.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:13.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:13.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:13.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:13.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:13.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:13.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:13.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:13.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.058][FUN] Functions in observer BiodbConfig: [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 [2026-01-31 16:02:14.059][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-01-31 16:02:14.067][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-01-31 16:02:14.080][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-01-31 16:02:14.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:14.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:14.087][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:14.096][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-01-31 16:02:14.098][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.099][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.100][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.101][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:14.102][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.103][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-01-31 16:02:14.104][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.105][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.106][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:14.107][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:14.108][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.108][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-01-31 16:02:14.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-01-31 16:02:14.110][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-01-31 16:02:14.111][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:14.112][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:14.112][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-01-31 16:02:14.112][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-01-31 16:02:14.113][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:14.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.116][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:14.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:14.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:14.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:14.120][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-01-31 16:02:14.120][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-01-31 16:02:14.120][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:14.121][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:14.122][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:14.123][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:14.129][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-01-31 16:02:14.130][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:14.132][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:14.133][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:14.135][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:14.155][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-01-31 16:02:14.170][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-01-31 16:02:14.178][biodb::testThat]
biodb.INFO [2026-01-31 16:02:14.179][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-31 16:02:14.180][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:14.181][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:14.185][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[2026-01-31 16:02:14.187][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:14.190][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-01-31 16:02:14.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:14.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:14.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:14.212][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:14.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:14.214][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:14.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:14.226][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.227][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.227][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.228][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.245][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.246][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.247][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.248][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.281][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.285][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.286][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.287][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.288][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.289][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.293][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.294][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.295][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.296][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.297][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.301][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.302][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.303][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.304][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.309][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.310][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.310][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.311][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.316][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.317][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.318][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.319][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.320][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.324][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.325][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.326][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.327][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.328][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.332][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.333][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.334][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.335][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.340][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.341][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.342][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.342][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.344][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.347][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:14.348][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:14.349][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.350][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.351][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:14.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:14.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.355][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:14.356][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:14.357][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.358][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:14.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:14.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.363][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.364][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.365][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.366][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.371][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.372][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.373][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.374][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.379][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.380][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.381][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.381][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.386][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:14.387][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:14.388][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.389][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.390][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:14.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:14.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.394][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:14.395][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:14.396][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.397][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.398][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:14.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:14.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.402][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-01-31 16:02:14.403][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:14.404][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.405][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.406][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-01-31 16:02:14.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:14.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.454][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.458][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.462][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:14.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.465][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.469][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.473][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:14.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.502][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:14.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.517][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:14.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.520][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:14.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:14.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.524][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:14.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:14.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.528][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:14.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:14.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.531][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:14.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:14.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.535][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:14.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:14.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.539][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:14.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:14.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:14.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:14.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.546][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:14.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:14.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.550][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:14.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:14.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:14.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:14.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.575][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.583][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.586][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:14.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.612][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.619][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.623][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.626][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.630][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.634][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:14.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:14.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.637][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:14.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:14.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.641][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:14.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:14.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.645][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-31 16:02:14.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.659][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-31 16:02:14.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:14.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:14.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:14.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.698][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.702][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.709][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:14.735][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-01-31 16:02:14.778][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:14.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:14.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.782][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:14.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:14.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:14.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:14.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:14.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.802][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.833][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.836][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.840][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:14.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.861][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.862][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.863][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.864][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:14.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:14.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.875][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.879][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.883][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.886][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.887][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.888][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.889][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.890][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:14.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.906][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.913][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.914][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.915][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.916][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:14.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.928][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.931][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.935][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.939][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.940][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.945][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.946][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.947][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:14.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.970][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.971][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:14.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.983][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.986][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.990][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.994][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.995][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.996][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:14.996][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:14.997][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:14.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:15.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:15.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:15.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:15.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:15.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:15.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.019][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:15.020][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:15.021][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.022][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:15.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:15.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.033][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:15.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:15.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.037][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:15.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:15.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.040][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:15.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:15.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.044][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:15.045][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:15.046][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.047][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.048][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:15.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:15.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.058][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:15.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:15.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:15.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:15.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.066][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:15.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:15.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.069][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:15.070][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:15.071][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.072][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.073][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:15.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:15.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.084][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.087][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.091][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.095][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.096][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.097][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.097][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.098][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.124][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.125][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.126][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.127][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.139][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.142][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.146][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.150][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.151][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.152][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.153][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.154][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.171][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.175][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.176][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.177][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.178][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.179][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.189][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.193][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.197][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.200][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.201][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.202][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.203][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.204][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.214][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:15.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:15.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.218][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:15.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.222][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:15.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:15.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.226][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:15.227][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:15.228][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.228][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.229][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:15.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:15.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:15.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:15.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:15.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:15.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:15.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:15.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.251][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:15.252][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:15.253][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.253][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:15.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:15.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.276][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.279][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.280][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.281][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.282][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.293][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.297][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.301][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.304][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.305][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.306][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.307][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.308][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.318][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:15.319][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:15.320][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.321][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.325][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.326][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:15.327][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.328][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.331][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.332][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:15.333][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.334][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:15.339][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:15.340][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.341][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.345][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:15.345][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:15.346][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.347][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.351][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.352][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:15.353][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.354][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.358][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.359][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:15.360][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.360][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.364][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.365][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:15.366][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.367][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.371][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:15.372][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:15.373][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.374][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.377][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:15.378][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:15.379][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.380][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.384][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:15.385][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:15.386][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.387][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.390][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.391][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:15.392][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.393][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.397][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:15.398][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:15.399][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.400][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.404][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.405][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:15.405][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.406][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.410][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:15.411][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:15.412][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.413][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.417][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:15.418][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:15.419][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.419][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.427][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:15.428][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:15.429][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.430][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:15.433][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:15.434][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:15.435][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.436][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:15.443][biodb::testThat]
biodb.INFO [2026-01-31 16:02:15.443][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-31 16:02:15.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:15.445][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:15.458][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-31 16:02:15.460][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:15.463][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:15.491][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-31 16:02:15.492][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-31 16:02:15.493][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:15.619][biodb::testThat]
biodb.INFO [2026-01-31 16:02:15.620][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-31 16:02:15.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:15.622][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:15.625][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:15.626][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:15.627][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:15.628][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:15.629][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-01-31 16:02:15.649][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-31 16:02:15.692][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:15.693][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:15.695][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-31 16:02:15.696][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-31 16:02:15.711][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:15.761][biodb::testThat]
biodb.INFO [2026-01-31 16:02:15.762][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-31 16:02:15.763][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:15.764][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:15.770][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-31 16:02:15.771][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:15.772][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:15.774][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-31 16:02:15.775][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-31 16:02:15.776][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:15.815][biodb::testThat]
biodb.INFO [2026-01-31 16:02:15.816][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-31 16:02:15.817][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:15.818][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:15.822][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-31 16:02:15.823][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:15.824][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:15.825][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-31 16:02:15.826][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-31 16:02:15.827][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:15.871][biodb::testThat]
biodb.INFO [2026-01-31 16:02:15.872][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-31 16:02:15.873][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:15.873][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:15.913][biodb::testThat]
biodb.INFO [2026-01-31 16:02:15.914][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-31 16:02:15.915][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:15.916][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:15.955][biodb::testThat]
biodb.INFO [2026-01-31 16:02:15.956][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:15.961][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:15.962][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:16.001][biodb::testThat]
biodb.INFO [2026-01-31 16:02:16.002][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:16.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:16.004][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-01-31 16:02:16.056][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:16.057][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:16.058][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.059][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.060][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:16.061][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:16.062][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.063][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.064][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:16.065][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:16.066][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.067][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.068][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:16.069][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:16.070][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.070][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.071][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:16.072][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:16.073][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.074][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:16.075][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:16.076][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:16.077][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:16.078][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:16.079][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:02:16.080][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-01-31 16:02:16.081][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:02:16.082][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:16.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:16.083][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:16.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:16.085][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:16.086][FUN] Functions in observer 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 1 | PASS 103 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ 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 1 | 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.16.0’
* 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:
  ── 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 1 | 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 ‘1.16.0’
** 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)