Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-28 23:55 -0500 (Sat, 28 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4891
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4681
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: 2026-02-28 09:55 -0500 (Sat, 28 Feb 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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: /Library/Frameworks/R.framework/Resources/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: 2026-02-28 16:01:22 -0500 (Sat, 28 Feb 2026)
EndedAt: 2026-02-28 16:02:58 -0500 (Sat, 28 Feb 2026)
EllapsedTime: 95.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-apple-darwin20

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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 [2026-02-28 16:02:53.452][biodb::testContext]
biodb.INFO [2026-02-28 16:02:53.456][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:53.457][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-28 16:02:53.459][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-28 16:02:53.460][biodb::testContext]
biodb.INFO [2026-02-28 16:02:53.466][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:53.469][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:53.477][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:53.478][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-28 16:02:53.479][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-28 16:02:53.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.484][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-28 16:02:53.512][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-28 16:02:53.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.516][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-28 16:02:53.518][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-28 16:02:53.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.522][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-28 16:02:53.524][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-28 16:02:53.525][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-28 16:02:53.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.530][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-28 16:02:53.531][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-28 16:02:53.532][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-28 16:02:53.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.537][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-28 16:02:53.539][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-28 16:02:53.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.544][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-28 16:02:53.545][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-28 16:02:53.546][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-28 16:02:53.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.551][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-28 16:02:53.552][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-28 16:02:53.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.557][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-28 16:02:53.559][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-28 16:02:53.560][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-28 16:02:53.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.565][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:53.566][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-28 16:02:53.568][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-28 16:02:53.569][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-28 16:02:53.570][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-28 16:02:53.572][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-28 16:02:53.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.577][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-28 16:02:53.578][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-28 16:02:53.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.583][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-28 16:02:53.585][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-28 16:02:53.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.590][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-28 16:02:53.591][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-28 16:02:53.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.596][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-28 16:02:53.597][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-28 16:02:53.598][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-28 16:02:53.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.603][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-28 16:02:53.604][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-28 16:02:53.615][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-28 16:02:53.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.620][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-28 16:02:53.621][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-28 16:02:53.623][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-28 16:02:53.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.630][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-28 16:02:53.674][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.701][self$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[2026-02-28 16:02:53.703][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.704][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:53.705][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.706][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.708][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.709][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.710][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:53.711][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:53.713][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.714][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-28 16:02:53.715][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:53.716][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.717][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.719][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:53.719][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:53.719][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:53.719][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:53.719][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:53.720][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:53.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:53.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:53.724][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:53.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:53.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:53.727][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.728][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.730][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:53.731][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:53.732][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.733][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.735][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-28 16:02:53.737][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.738][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:53.739][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.740][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:53.742][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.743][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.744][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.745][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.747][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:53.748][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:53.749][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.750][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-28 16:02:53.752][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:53.753][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.754][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.755][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:53.755][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-28 16:02:53.755][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-28 16:02:53.755][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-28 16:02:53.755][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-28 16:02:53.757][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:53.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:53.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:53.760][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:53.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:53.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:53.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.765][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:53.767][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:53.768][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.770][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.771][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-28 16:02:53.773][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.775][self$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[2026-02-28 16:02:53.776][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.777][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:53.778][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.780][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.781][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.782][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.783][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-28 16:02:53.784][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:53.786][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.787][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-28 16:02:53.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:53.789][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.791][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.792][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.793][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:53.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:53.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:53.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:53.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:53.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:53.800][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.801][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.803][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:53.804][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:53.805][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.806][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.808][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-28 16:02:53.810][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.811][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-28 16:02:53.812][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:53.815][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.816][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.817][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.818][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.820][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-28 16:02:53.821][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:53.822][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.823][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-28 16:02:53.825][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:53.826][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.827][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:53.828][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.830][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-28 16:02:53.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:53.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:53.833][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:53.834][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:53.835][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:53.837][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:53.838][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.839][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:53.840][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:53.841][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:53.843][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:53.846][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:53.848][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.849][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[2026-02-28 16:02:53.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.882][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[2026-02-28 16:02:53.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.888][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[2026-02-28 16:02:53.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.921][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[2026-02-28 16:02:53.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.927][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[2026-02-28 16:02:53.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:53.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:53.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:53.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:53.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:53.940][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-28 16:02:53.944][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-28 16:02:53.946][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-28 16:02:53.952][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-28 16:02:53.954][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-28 16:02:53.956][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-28 16:02:53.957][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:53.959][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:53.961][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-28 16:02:53.962][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-28 16:02:53.964][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-28 16:02:53.966][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-28 16:02:53.967][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-28 16:02:53.969][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-28 16:02:53.971][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-28 16:02:53.972][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:53.974][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-28 16:02:53.976][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-28 16:02:53.977][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-28 16:02:53.979][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-28 16:02:53.981][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-28 16:02:53.983][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-28 16:02:53.984][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-28 16:02:53.986][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-28 16:02:53.988][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-28 16:02:53.990][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-28 16:02:53.991][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-28 16:02:53.993][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-28 16:02:53.995][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-28 16:02:53.997][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-28 16:02:53.998][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-28 16:02:54.000][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-28 16:02:54.002][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-28 16:02:54.003][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-28 16:02:54.005][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-28 16:02:54.007][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-28 16:02:54.009][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-28 16:02:54.010][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-28 16:02:54.012][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-28 16:02:54.014][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-28 16:02:54.016][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-28 16:02:54.018][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-28 16:02:54.019][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-28 16:02:54.021][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-28 16:02:54.023][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-28 16:02:54.025][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-28 16:02:54.026][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-28 16:02:54.028][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-28 16:02:54.030][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-28 16:02:54.032][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-28 16:02:54.033][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-28 16:02:54.035][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-28 16:02:54.037][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-28 16:02:54.039][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-28 16:02:54.040][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-28 16:02:54.042][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-28 16:02:54.044][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-28 16:02:54.046][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-28 16:02:54.048][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-28 16:02:54.049][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-28 16:02:54.051][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-28 16:02:54.053][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-28 16:02:54.054][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-28 16:02:54.056][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-28 16:02:54.058][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-28 16:02:54.060][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-28 16:02:54.061][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-28 16:02:54.063][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-28 16:02:54.065][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-28 16:02:54.066][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-28 16:02:54.068][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-28 16:02:54.070][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-28 16:02:54.072][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-28 16:02:54.074][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-28 16:02:54.076][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-28 16:02:54.077][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-28 16:02:54.079][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-28 16:02:54.081][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-28 16:02:54.083][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-28 16:02:54.085][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-28 16:02:54.087][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-28 16:02:54.088][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-28 16:02:54.090][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-28 16:02:54.098][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-28 16:02:54.100][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-28 16:02:54.103][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-28 16:02:54.105][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.107][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.245][FUN] Functions in observer BiodbConfig: [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 [2026-02-28 16:02:54.246][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-02-28 16:02:54.256][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-02-28 16:02:54.276][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-02-28 16:02:54.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-28 16:02:54.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-28 16:02:54.287][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-02-28 16:02:54.300][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-02-28 16:02:54.302][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:54.304][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-02-28 16:02:54.305][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:54.306][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-28 16:02:54.307][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:54.309][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-02-28 16:02:54.310][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:54.312][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-28 16:02:54.313][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-28 16:02:54.314][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-28 16:02:54.316][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:54.317][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-02-28 16:02:54.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-02-28 16:02:54.320][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-02-28 16:02:54.321][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-28 16:02:54.323][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-28 16:02:54.323][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-02-28 16:02:54.323][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-02-28 16:02:54.324][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-28 16:02:54.325][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:54.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:54.328][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-28 16:02:54.329][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-28 16:02:54.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-28 16:02:54.332][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-28 16:02:54.333][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-02-28 16:02:54.333][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-02-28 16:02:54.335][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-28 16:02:54.336][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-28 16:02:54.337][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-28 16:02:54.339][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-28 16:02:54.347][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-02-28 16:02:54.349][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-28 16:02:54.351][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-28 16:02:54.353][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-28 16:02:54.355][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-28 16:02:54.379][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-02-28 16:02:54.395][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-02-28 16:02:54.405][biodb::testThat]
biodb.INFO [2026-02-28 16:02:54.406][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-28 16:02:54.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:54.409][biodb::testThat]
biodb.TRACE[2026-02-28 16:02:54.413][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-02-28 16:02:54.415][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-02-28 16:02:54.419][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-02-28 16:02:54.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-28 16:02:54.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:54.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:54.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:54.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:54.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:54.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-02-28 16:02:54.461][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:54.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:54.464][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.465][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:54.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:54.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.499][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:54.500][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:54.501][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.502][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.538][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:54.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:54.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.544][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.545][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.546][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.548][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.549][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.554][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.556][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.557][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.558][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.560][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.565][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.567][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.568][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.569][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.576][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.578][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.579][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.580][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.588][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.589][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.590][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.592][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.597][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:54.598][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:54.599][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.601][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.602][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:54.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:54.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.607][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.609][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.610][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.611][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.618][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.619][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.620][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.621][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.623][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.628][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:54.629][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:54.630][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.632][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.633][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:54.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:54.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.638][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:54.640][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:54.641][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.642][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:54.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:54.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.649][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.650][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.651][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.653][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.659][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.661][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.662][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.663][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.670][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:54.671][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:54.672][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.673][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:54.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:54.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.680][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:54.681][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:54.682][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.684][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.685][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:54.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:54.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.690][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:54.691][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:54.693][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.694][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:54.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:54.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.700][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-02-28 16:02:54.702][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:54.703][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.704][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.706][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-02-28 16:02:54.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:54.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:54.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:54.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:54.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:54.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:54.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:54.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.776][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.782][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.787][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:54.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.792][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.797][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.802][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:54.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:54.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:54.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.837][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.842][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.847][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:54.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.852][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.857][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.862][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:54.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:54.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:54.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.872][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:54.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:54.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:54.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:54.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.882][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:54.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:54.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.887][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:54.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:54.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.892][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:54.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:54.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:54.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:54.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.902][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:54.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:54.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.907][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:54.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:54.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:54.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:54.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.917][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:54.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:54.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:54.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:54.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.940][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:54.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.945][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.950][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.955][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:54.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:54.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:54.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:54.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:54.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:54.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:54.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:54.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.990][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:54.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:54.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:54.995][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:54.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:54.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:54.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.000][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.005][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.010][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.015][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.020][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:55.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:55.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:55.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:55.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.030][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:55.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:55.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.035][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-28 16:02:55.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.054][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-28 16:02:55.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.108][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.113][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.122][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:55.190][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-02-28 16:02:55.193][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:55.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:55.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.198][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-28 16:02:55.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-28 16:02:55.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.203][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:55.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-28 16:02:55.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.208][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:55.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-28 16:02:55.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.225][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.268][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.273][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.278][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-28 16:02:55.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.307][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.308][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.309][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.311][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.327][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.332][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.337][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.342][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.344][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.345][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.346][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.347][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:55.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.378][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.379][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.381][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.382][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:55.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.402][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.407][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.413][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.419][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.421][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.422][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.423][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:55.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.455][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.456][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.458][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.459][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.476][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.481][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.486][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.491][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.493][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.494][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.495][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.496][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:55.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.527][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.528][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.529][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.530][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:55.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:55.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.547][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:55.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:55.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.552][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:55.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:55.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.557][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:55.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:55.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.562][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:55.563][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:55.565][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.566][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.567][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:55.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:55.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.583][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:55.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:55.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:55.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:55.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:55.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:55.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.601][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:55.602][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:55.603][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.604][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.606][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:55.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:55.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.626][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.631][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.636][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.641][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.642][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.643][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.644][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.646][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.676][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.678][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.679][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.680][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:55.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.697][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.702][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.707][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.712][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.713][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.714][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.716][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:55.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.732][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.738][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.743][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.750][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.751][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.752][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.754][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.757][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:55.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.776][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.781][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.786][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.791][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.792][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.793][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.795][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.796][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:55.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.811][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:55.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:55.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.817][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:55.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:55.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.821][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:55.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:55.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.826][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:55.828][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:55.829][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.830][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.831][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:55.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:55.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:55.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:55.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:55.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:55.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:55.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:55.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.866][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:55.868][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:55.869][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.870][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:55.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:55.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.905][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.907][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.908][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.909][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:55.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.926][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.932][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.937][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.942][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.943][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.944][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.946][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.947][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.962][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-28 16:02:55.964][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-28 16:02:55.965][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.966][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.972][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.974][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-28 16:02:55.975][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.976][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.983][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.984][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-28 16:02:55.985][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.987][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:55.993][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-28 16:02:55.996][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:55.997][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.004][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:56.005][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-28 16:02:56.006][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.008][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.014][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:56.016][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-28 16:02:56.017][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.018][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.025][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:56.027][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-28 16:02:56.028][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.029][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.036][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:56.037][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-28 16:02:56.038][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.040][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.046][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:56.048][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:56.049][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.050][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.057][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-28 16:02:56.058][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-28 16:02:56.060][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.061][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.067][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-28 16:02:56.069][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-28 16:02:56.070][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.071][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.078][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-28 16:02:56.080][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-28 16:02:56.081][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.082][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.093][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:56.095][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-28 16:02:56.096][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.097][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.103][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:56.105][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-28 16:02:56.106][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.107][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.113][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:56.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:56.116][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.117][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.123][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:56.125][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-28 16:02:56.126][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.127][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.133][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:56.135][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:56.136][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.137][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:56.144][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-28 16:02:56.145][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-28 16:02:56.147][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.148][ef$get] fields variable is a list.
biodb.INFO [2026-02-28 16:02:56.158][biodb::testThat]
biodb.INFO [2026-02-28 16:02:56.160][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-28 16:02:56.161][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:56.162][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:56.182][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-28 16:02:56.187][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-28 16:02:56.190][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-28 16:02:56.235][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-28 16:02:56.237][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-28 16:02:56.238][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-28 16:02:56.441][biodb::testThat]
biodb.INFO [2026-02-28 16:02:56.443][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-28 16:02:56.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:56.445][biodb::testThat]
biodb.TRACE[2026-02-28 16:02:56.449][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:56.451][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:56.452][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:56.454][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-28 16:02:56.456][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-02-28 16:02:56.489][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-28 16:02:56.558][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-28 16:02:56.560][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-28 16:02:56.561][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-28 16:02:56.563][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-28 16:02:56.580][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-28 16:02:56.652][biodb::testThat]
biodb.INFO [2026-02-28 16:02:56.653][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-28 16:02:56.655][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:56.656][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:56.666][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-28 16:02:56.668][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-28 16:02:56.669][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-28 16:02:56.671][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-28 16:02:56.673][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-28 16:02:56.674][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-28 16:02:56.736][biodb::testThat]
biodb.INFO [2026-02-28 16:02:56.738][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-28 16:02:56.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:56.740][biodb::testThat]
biodb.DEBUG[2026-02-28 16:02:56.745][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-28 16:02:56.747][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-28 16:02:56.748][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-28 16:02:56.750][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-28 16:02:56.751][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-28 16:02:56.753][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-28 16:02:56.822][biodb::testThat]
biodb.INFO [2026-02-28 16:02:56.823][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-28 16:02:56.824][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:56.825][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-28 16:02:56.890][biodb::testThat]
biodb.INFO [2026-02-28 16:02:56.892][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-28 16:02:56.895][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:56.896][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-28 16:02:56.968][biodb::testThat]
biodb.INFO [2026-02-28 16:02:56.969][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:56.970][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:56.971][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-28 16:02:57.031][biodb::testThat]
biodb.INFO [2026-02-28 16:02:57.032][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-28 16:02:57.033][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-28 16:02:57.035][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-02-28 16:02:57.125][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:57.126][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:57.128][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:57.129][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:57.131][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:57.134][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:57.136][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:57.138][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:57.139][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:57.140][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:57.141][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:57.143][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:57.145][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-28 16:02:57.147][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-28 16:02:57.149][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:57.150][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:57.151][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-28 16:02:57.153][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-28 16:02:57.154][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:57.155][ef$get] fields variable is a list.
biodb.TRACE[2026-02-28 16:02:57.156][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:57.158][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-28 16:02:57.159][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-28 16:02:57.160][ef$get] fields variable is a list.
biodb.INFO [2026-02-28 16:02:57.162][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-28 16:02:57.163][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-02-28 16:02:57.164][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-28 16:02:57.165][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-28 16:02:57.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-28 16:02:57.167][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-28 16:02:57.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-28 16:02:57.170][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-28 16:02:57.171][FUN] Functions in observer 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:
###
###   /Library/Frameworks/R.framework/Resources/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 ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* 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 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, 1 WARNING, 1 NOTE
See
  ‘/Users/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/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)