Back to Long Tests report for BioC 3.22

This page was generated on 2026-04-04 23:55 -0400 (Sat, 04 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4897
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4691
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: 2026-04-04 09:55 -0400 (Sat, 04 Apr 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 -0400 (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: 2026-04-04 16:01:08 -0400 (Sat, 04 Apr 2026)
EndedAt: 2026-04-04 16:02:16 -0400 (Sat, 04 Apr 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 [2026-04-04 16:02:12.340][biodb::testContext]
biodb.INFO [2026-04-04 16:02:12.342][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:12.343][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-04-04 16:02:12.344][biodb::testContext] ********************************************************************************
biodb.INFO [2026-04-04 16:02:12.344][biodb::testContext]
biodb.INFO [2026-04-04 16:02:12.350][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:12.352][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:12.358][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:12.359][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-04-04 16:02:12.360][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.363][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-04-04 16:02:12.379][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.383][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-04-04 16:02:12.384][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.387][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-04-04 16:02:12.388][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-04-04 16:02:12.389][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-04-04 16:02:12.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.393][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-04-04 16:02:12.394][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-04-04 16:02:12.394][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.398][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-04-04 16:02:12.399][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-04-04 16:02:12.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.402][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-04-04 16:02:12.403][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-04-04 16:02:12.404][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-04-04 16:02:12.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.407][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-04-04 16:02:12.408][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.412][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-04-04 16:02:12.413][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-04-04 16:02:12.414][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-04-04 16:02:12.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.417][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:12.418][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-04-04 16:02:12.419][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-04-04 16:02:12.420][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-04-04 16:02:12.421][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-04-04 16:02:12.422][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-04-04 16:02:12.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.425][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-04-04 16:02:12.426][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-04-04 16:02:12.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.430][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-04-04 16:02:12.431][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-04-04 16:02:12.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.434][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-04-04 16:02:12.435][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-04-04 16:02:12.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.438][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-04-04 16:02:12.439][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-04-04 16:02:12.440][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-04-04 16:02:12.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.444][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-04-04 16:02:12.445][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-04-04 16:02:12.449][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-04-04 16:02:12.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.452][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-04-04 16:02:12.453][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-04-04 16:02:12.454][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-04-04 16:02:12.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.460][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-04-04 16:02:12.490][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.510][self$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[2026-04-04 16:02:12.511][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.512][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:12.513][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.514][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.515][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.516][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.517][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:12.518][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:12.519][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.519][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-04-04 16:02:12.520][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:12.521][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.522][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.523][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:12.523][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:12.523][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:12.523][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:12.523][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:12.524][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:12.525][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.527][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:12.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.529][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.530][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.531][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:12.532][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:12.533][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.534][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.535][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-04-04 16:02:12.537][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.538][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:12.538][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.539][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:12.540][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.541][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.542][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.543][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.544][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:12.545][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:12.546][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.547][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-04-04 16:02:12.548][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:12.549][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.550][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.551][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:12.551][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-04-04 16:02:12.551][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-04-04 16:02:12.551][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-04-04 16:02:12.551][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-04-04 16:02:12.552][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:12.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.554][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:12.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.557][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.558][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.559][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:12.559][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:12.560][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.561][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.562][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-04-04 16:02:12.564][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.565][self$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[2026-04-04 16:02:12.566][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.567][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:12.568][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.569][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.570][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.571][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.572][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-04-04 16:02:12.572][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:12.573][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.574][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-04-04 16:02:12.575][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:12.576][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.577][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.578][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.579][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:12.580][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.582][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:12.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.584][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.585][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.586][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:12.587][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:12.588][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.589][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.590][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-04-04 16:02:12.591][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.592][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-04-04 16:02:12.593][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.594][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:12.595][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.596][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.597][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.598][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.599][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-04-04 16:02:12.600][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:12.601][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.602][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-04-04 16:02:12.603][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:12.604][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.604][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.605][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.606][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-04-04 16:02:12.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.609][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:12.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:12.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:12.612][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.612][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:12.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:12.615][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.616][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:12.620][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:12.620][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.689][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-04-04 16:02:12.693][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-04-04 16:02:12.695][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-04-04 16:02:12.696][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-04-04 16:02:12.697][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-04-04 16:02:12.699][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:12.700][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:12.701][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:12.702][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-04-04 16:02:12.704][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:12.709][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:12.711][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-04-04 16:02:12.712][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-04-04 16:02:12.713][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-04-04 16:02:12.714][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-04-04 16:02:12.716][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:12.717][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-04-04 16:02:12.718][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-04-04 16:02:12.719][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-04-04 16:02:12.721][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-04-04 16:02:12.722][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-04-04 16:02:12.723][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-04-04 16:02:12.732][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-04-04 16:02:12.734][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-04-04 16:02:12.736][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-04-04 16:02:12.738][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-04-04 16:02:12.739][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-04-04 16:02:12.741][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-04-04 16:02:12.742][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-04-04 16:02:12.744][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-04-04 16:02:12.746][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-04-04 16:02:12.747][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-04-04 16:02:12.749][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-04-04 16:02:12.751][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-04-04 16:02:12.752][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-04-04 16:02:12.754][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-04-04 16:02:12.755][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-04-04 16:02:12.757][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-04-04 16:02:12.758][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-04-04 16:02:12.760][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-04-04 16:02:12.761][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-04-04 16:02:12.763][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-04-04 16:02:12.764][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-04-04 16:02:12.766][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-04-04 16:02:12.767][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-04-04 16:02:12.769][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-04-04 16:02:12.770][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-04-04 16:02:12.771][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-04-04 16:02:12.773][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-04-04 16:02:12.774][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-04-04 16:02:12.776][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-04-04 16:02:12.777][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-04-04 16:02:12.779][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-04-04 16:02:12.780][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-04-04 16:02:12.782][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-04-04 16:02:12.783][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-04-04 16:02:12.785][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-04-04 16:02:12.786][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-04-04 16:02:12.788][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-04-04 16:02:12.789][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-04-04 16:02:12.791][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-04-04 16:02:12.792][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-04-04 16:02:12.793][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-04-04 16:02:12.795][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-04-04 16:02:12.796][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-04-04 16:02:12.798][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-04-04 16:02:12.799][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-04-04 16:02:12.801][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-04-04 16:02:12.802][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-04-04 16:02:12.803][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-04-04 16:02:12.805][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-04-04 16:02:12.806][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-04-04 16:02:12.808][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-04-04 16:02:12.809][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-04-04 16:02:12.811][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-04-04 16:02:12.812][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-04-04 16:02:12.814][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-04-04 16:02:12.815][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-04-04 16:02:12.817][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-04-04 16:02:12.818][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-04-04 16:02:12.819][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-04-04 16:02:12.821][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-04-04 16:02:12.822][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-04-04 16:02:12.829][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-04-04 16:02:12.831][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-04-04 16:02:12.835][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-04-04 16:02:12.836][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.838][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.957][FUN] Functions in observer BiodbConfig: [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 [2026-04-04 16:02:12.958][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-04-04 16:02:12.965][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-04-04 16:02:12.978][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-04-04 16:02:12.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-04-04 16:02:12.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:12.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:12.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:12.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:12.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:12.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-04-04 16:02:12.986][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-04-04 16:02:12.995][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-04-04 16:02:12.996][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:12.997][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-04-04 16:02:12.998][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:12.999][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-04-04 16:02:13.000][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:13.001][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-04-04 16:02:13.002][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.003][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.004][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-04-04 16:02:13.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-04-04 16:02:13.006][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.007][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-04-04 16:02:13.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-04-04 16:02:13.009][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-04-04 16:02:13.010][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-04-04 16:02:13.011][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-04-04 16:02:13.011][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-04-04 16:02:13.011][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-04-04 16:02:13.011][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-04-04 16:02:13.012][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.014][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-04-04 16:02:13.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-04-04 16:02:13.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-04-04 16:02:13.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-04-04 16:02:13.018][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-04-04 16:02:13.018][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-04-04 16:02:13.019][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-04-04 16:02:13.019][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-04-04 16:02:13.020][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-04-04 16:02:13.021][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-04-04 16:02:13.027][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-04-04 16:02:13.028][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-04-04 16:02:13.029][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-04-04 16:02:13.031][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-04-04 16:02:13.032][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-04-04 16:02:13.053][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-04-04 16:02:13.067][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-04-04 16:02:13.075][biodb::testThat]
biodb.INFO [2026-04-04 16:02:13.076][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-04-04 16:02:13.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:13.078][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:13.081][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[2026-04-04 16:02:13.083][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-04-04 16:02:13.086][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-04-04 16:02:13.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-04-04 16:02:13.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:13.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:13.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:13.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:13.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:13.110][FUN] Functions in observer BiodbConfig: [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[2026-04-04 16:02:13.121][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.122][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.123][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.124][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.140][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.141][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.142][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.143][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.176][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.180][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.181][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.182][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.183][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.184][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.188][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.189][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.190][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.191][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.192][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.196][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.197][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.198][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.198][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.203][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.204][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.205][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.206][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.211][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.212][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.213][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.214][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.215][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.219][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.220][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.221][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.221][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.223][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.226][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.227][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.228][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.229][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.230][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.234][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.235][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.236][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.237][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.242][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.243][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.244][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.245][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.246][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.249][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:13.250][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:13.251][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.252][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:13.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:13.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.257][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.258][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.259][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.260][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.265][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.266][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.267][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.268][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.273][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.273][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.274][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.275][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.280][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.281][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.282][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.283][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.284][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.288][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:13.289][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:13.290][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.291][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.292][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:13.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:13.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.296][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-04-04 16:02:13.297][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:13.297][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.298][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.299][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-04-04 16:02:13.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:13.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.348][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.352][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.356][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.359][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.363][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.367][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:13.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.393][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.396][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:13.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.408][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.411][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:13.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.415][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:13.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:13.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.419][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:13.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:13.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:13.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:13.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.426][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.430][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.434][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.441][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.445][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:13.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:13.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.452][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:13.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:13.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.456][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:13.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:13.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.460][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.471][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.478][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.482][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:13.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.500][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.508][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.512][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.515][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.519][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.523][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.527][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.530][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:13.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:13.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.534][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:13.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:13.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.538][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:13.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:13.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.541][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-04-04 16:02:13.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.556][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-04-04 16:02:13.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:13.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.595][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.599][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.606][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:13.632][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-04-04 16:02:13.675][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:13.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:13.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-04-04 16:02:13.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-04-04 16:02:13.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.683][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:13.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-04-04 16:02:13.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:13.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-04-04 16:02:13.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.699][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.730][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.733][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.737][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-04-04 16:02:13.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.758][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.759][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.760][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.761][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:13.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:13.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.772][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.776][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.780][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.784][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.785][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.786][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.786][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.787][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:13.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.809][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.810][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.811][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.812][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.827][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.835][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.836][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.841][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.842][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.842][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:13.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.864][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.865][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.866][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.867][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:13.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.878][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.882][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.886][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.889][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.890][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.891][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.892][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.893][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:13.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.904][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.915][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.916][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.917][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.918][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:13.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:13.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.929][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.933][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.936][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.940][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.941][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.942][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.943][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.944][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:13.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:13.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.962][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.965][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.966][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.967][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.968][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.969][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:13.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:13.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.980][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.983][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.987][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.991][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.992][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.993][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.994][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:13.994][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:13.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:13.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.020][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.021][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.022][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.023][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.034][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.038][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.045][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.046][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.047][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.048][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.049][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.060][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.067][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.071][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.072][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.073][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.074][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.074][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.096][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.097][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.098][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.099][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.100][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.110][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:14.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:14.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.114][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:14.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:14.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.118][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:14.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:14.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.121][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:14.122][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:14.123][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.124][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:14.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:14.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:14.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:14.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.139][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:14.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:14.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:14.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:14.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.147][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:14.148][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:14.148][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.149][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:14.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:14.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.175][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.176][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.177][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.178][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.189][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.193][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.197][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.200][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.201][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.202][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.203][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.204][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.214][ef$get] Asked field names are: accession.
biodb.TRACE[2026-04-04 16:02:14.215][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-04-04 16:02:14.216][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.217][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.221][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-04-04 16:02:14.222][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-04-04 16:02:14.223][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.224][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.227][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.228][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-04-04 16:02:14.229][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.230][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.234][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-04-04 16:02:14.235][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-04-04 16:02:14.236][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.237][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.241][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:14.242][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-04-04 16:02:14.243][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.243][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.247][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.248][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-04-04 16:02:14.249][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.250][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.254][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.255][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-04-04 16:02:14.256][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.257][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.261][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.262][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-04-04 16:02:14.262][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.263][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.267][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:14.268][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:14.269][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.270][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.274][ef$get] Asked field names are: formula.
biodb.TRACE[2026-04-04 16:02:14.275][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-04-04 16:02:14.276][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.277][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.280][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-04-04 16:02:14.281][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-04-04 16:02:14.282][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.283][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.287][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.288][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-04-04 16:02:14.289][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.290][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.293][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:14.294][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-04-04 16:02:14.295][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.296][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.300][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.301][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-04-04 16:02:14.302][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.303][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.307][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:14.308][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:14.308][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.309][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.313][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:14.314][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-04-04 16:02:14.315][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.316][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.324][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:14.325][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:14.326][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.326][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.330][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-04-04 16:02:14.331][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-04-04 16:02:14.332][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.333][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:14.339][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.340][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-04-04 16:02:14.341][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.342][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:14.355][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-04-04 16:02:14.358][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:14.361][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:14.388][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-04-04 16:02:14.390][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-04-04 16:02:14.390][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:14.517][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.518][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-04-04 16:02:14.519][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.520][biodb::testThat]
biodb.TRACE[2026-04-04 16:02:14.523][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:14.524][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:14.525][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.525][ef$get] fields variable is a list.
biodb.DEBUG[2026-04-04 16:02:14.527][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-04-04 16:02:14.546][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-04-04 16:02:14.589][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:14.590][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:14.592][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-04-04 16:02:14.593][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-04-04 16:02:14.608][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:14.657][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.658][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-04-04 16:02:14.659][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.660][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:14.667][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-04-04 16:02:14.668][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:14.669][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:14.670][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-04-04 16:02:14.671][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-04-04 16:02:14.672][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:14.713][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.714][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-04-04 16:02:14.715][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.715][biodb::testThat]
biodb.DEBUG[2026-04-04 16:02:14.719][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-04-04 16:02:14.720][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-04-04 16:02:14.721][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-04-04 16:02:14.723][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-04-04 16:02:14.724][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-04-04 16:02:14.725][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:14.768][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.769][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-04-04 16:02:14.770][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.771][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:14.811][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.812][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-04-04 16:02:14.813][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.814][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:14.858][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.859][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:14.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.860][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-04-04 16:02:14.900][biodb::testThat]
biodb.INFO [2026-04-04 16:02:14.901][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-04-04 16:02:14.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-04-04 16:02:14.903][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-04-04 16:02:14.956][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:14.957][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:14.958][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.959][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.960][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:14.961][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:14.962][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.963][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.964][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:14.965][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:14.966][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.966][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.968][ef$get] Asked field names are: name.
biodb.TRACE[2026-04-04 16:02:14.969][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-04-04 16:02:14.969][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.970][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.971][ef$get] Asked field names are: description.
biodb.TRACE[2026-04-04 16:02:14.972][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-04-04 16:02:14.973][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.974][ef$get] fields variable is a list.
biodb.TRACE[2026-04-04 16:02:14.975][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:14.976][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-04-04 16:02:14.977][ef$get] 1 fields were returned.
biodb.TRACE[2026-04-04 16:02:14.978][ef$get] fields variable is a list.
biodb.INFO [2026-04-04 16:02:14.979][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-04-04 16:02:14.980][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-04-04 16:02:14.981][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-04-04 16:02:14.982][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-04-04 16:02:14.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-04-04 16:02:14.983][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-04-04 16:02:14.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-04-04 16:02:14.985][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-04-04 16:02:14.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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 24.04.4 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 13.3.0-6ubuntu2~24.04.1) 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 13.3.0-6ubuntu2~24.04.1) 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)