Back to Long Tests report for BioC 3.22

This page was generated on 2026-01-17 23:55 -0500 (Sat, 17 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4886
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4676
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-01-17 09:55 -0500 (Sat, 17 Jan 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on 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: 2026-01-17 16:01:42 -0500 (Sat, 17 Jan 2026)
EndedAt: 2026-01-17 16:03:11 -0500 (Sat, 17 Jan 2026)
EllapsedTime: 88.4 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"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2026-01-17 16:03:06.440][biodb::testContext]
biodb.INFO [2026-01-17 16:03:06.444][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-17 16:03:06.445][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-01-17 16:03:06.446][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-17 16:03:06.447][biodb::testContext]
biodb.INFO [2026-01-17 16:03:06.454][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-17 16:03:06.456][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-17 16:03:06.469][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:03:06.470][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-17 16:03:06.471][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-17 16:03:06.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.476][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-17 16:03:06.500][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-17 16:03:06.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.505][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-17 16:03:06.506][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-17 16:03:06.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.511][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-17 16:03:06.512][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-17 16:03:06.513][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-17 16:03:06.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.518][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-17 16:03:06.519][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-17 16:03:06.520][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-17 16:03:06.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.525][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-17 16:03:06.526][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-17 16:03:06.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.531][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-17 16:03:06.532][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-17 16:03:06.533][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-17 16:03:06.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.538][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-17 16:03:06.539][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-17 16:03:06.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.542][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[2026-01-17 16:03:06.543][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-17 16:03:06.545][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-17 16:03:06.546][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-17 16:03:06.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.550][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-17 16:03:06.551][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-17 16:03:06.553][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-17 16:03:06.554][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-17 16:03:06.555][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-17 16:03:06.556][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-17 16:03:06.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.561][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-17 16:03:06.562][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-17 16:03:06.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.567][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-17 16:03:06.568][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-17 16:03:06.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.572][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-17 16:03:06.574][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-17 16:03:06.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.578][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-17 16:03:06.579][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-17 16:03:06.581][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-17 16:03:06.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.585][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-17 16:03:06.586][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-17 16:03:06.597][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-17 16:03:06.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.602][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-17 16:03:06.603][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-17 16:03:06.604][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-17 16:03:06.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.612][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-17 16:03:06.656][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.684][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-17 16:03:06.685][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:06.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.689][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.690][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.692][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.693][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-17 16:03:06.694][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:06.695][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.697][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-17 16:03:06.698][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:06.699][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.700][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.702][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-17 16:03:06.702][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-17 16:03:06.702][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-17 16:03:06.702][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-17 16:03:06.702][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-17 16:03:06.703][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:03:06.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:06.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:06.707][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:06.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:06.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:06.710][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.711][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:06.714][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:06.715][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.716][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.718][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-17 16:03:06.720][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.722][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-17 16:03:06.723][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.725][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:06.726][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.728][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.729][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.730][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.732][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-17 16:03:06.733][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:06.734][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.735][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-17 16:03:06.737][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:06.738][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.739][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.741][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-17 16:03:06.741][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-17 16:03:06.741][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-17 16:03:06.741][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-17 16:03:06.741][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-17 16:03:06.742][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:03:06.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:06.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:06.746][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:06.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:06.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:06.749][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.750][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:06.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:06.754][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.755][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.757][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-17 16:03:06.759][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.761][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-17 16:03:06.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.763][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:06.764][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.767][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.768][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.769][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-17 16:03:06.771][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:06.772][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.773][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-17 16:03:06.775][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:06.776][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.777][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.778][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.780][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:03:06.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:06.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:06.783][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:06.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:06.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:06.787][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.788][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.789][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:06.790][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:06.792][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.793][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.794][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-17 16:03:06.797][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.798][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-17 16:03:06.799][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.800][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:06.802][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.803][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.804][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.805][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.807][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-17 16:03:06.808][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:06.809][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.811][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-17 16:03:06.812][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:06.813][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.814][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:06.816][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.817][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-17 16:03:06.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:06.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:06.820][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:06.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:06.823][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:06.824][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:06.825][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.827][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:06.828][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:06.829][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:06.830][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:06.834][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:03:06.836][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.849][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[2026-01-17 16:03:06.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.854][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[2026-01-17 16:03:06.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:06.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:06.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:06.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:06.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:06.937][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-17 16:03:06.942][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-17 16:03:06.943][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-17 16:03:06.945][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-17 16:03:06.947][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-17 16:03:06.948][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-17 16:03:06.950][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-17 16:03:06.952][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-17 16:03:06.953][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-17 16:03:06.955][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-17 16:03:06.957][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-17 16:03:06.958][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-17 16:03:06.960][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-17 16:03:06.962][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-17 16:03:06.963][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-17 16:03:06.965][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-17 16:03:06.967][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-17 16:03:06.969][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-17 16:03:06.970][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-17 16:03:06.972][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-17 16:03:06.974][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-17 16:03:06.976][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-17 16:03:06.977][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-17 16:03:06.979][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-17 16:03:06.981][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-17 16:03:06.983][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-17 16:03:06.984][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-17 16:03:06.986][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-17 16:03:06.988][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-17 16:03:06.989][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-17 16:03:06.991][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-17 16:03:06.993][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-17 16:03:06.995][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-17 16:03:06.997][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-17 16:03:06.999][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-17 16:03:07.000][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-17 16:03:07.002][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-17 16:03:07.004][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-17 16:03:07.006][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-17 16:03:07.007][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-17 16:03:07.009][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-17 16:03:07.011][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-17 16:03:07.013][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-17 16:03:07.014][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-17 16:03:07.016][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-17 16:03:07.018][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-17 16:03:07.020][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-17 16:03:07.021][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-17 16:03:07.023][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-17 16:03:07.025][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-17 16:03:07.027][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-17 16:03:07.028][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-17 16:03:07.030][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-17 16:03:07.032][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-17 16:03:07.034][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-17 16:03:07.035][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-17 16:03:07.037][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-17 16:03:07.039][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-17 16:03:07.041][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-17 16:03:07.043][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-17 16:03:07.044][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-17 16:03:07.046][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-17 16:03:07.048][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-17 16:03:07.050][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-17 16:03:07.052][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-17 16:03:07.053][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-17 16:03:07.055][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-17 16:03:07.057][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-17 16:03:07.059][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-17 16:03:07.060][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-17 16:03:07.062][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-17 16:03:07.064][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-17 16:03:07.066][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-17 16:03:07.068][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-17 16:03:07.069][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-17 16:03:07.071][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-17 16:03:07.073][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-17 16:03:07.075][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-17 16:03:07.077][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-17 16:03:07.079][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-17 16:03:07.081][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-17 16:03:07.083][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-17 16:03:07.085][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-17 16:03:07.093][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-17 16:03:07.096][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-17 16:03:07.099][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-17 16:03:07.100][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.103][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.193][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[2026-01-17 16:03:07.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2026-01-17 16:03:07.240][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-01-17 16:03:07.250][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-01-17 16:03:07.268][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-01-17 16:03:07.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-17 16:03:07.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-17 16:03:07.278][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-01-17 16:03:07.291][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-01-17 16:03:07.293][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:07.295][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-01-17 16:03:07.296][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:07.297][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-17 16:03:07.298][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:07.300][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-01-17 16:03:07.301][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:07.302][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-17 16:03:07.303][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-17 16:03:07.305][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-17 16:03:07.306][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:07.307][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-01-17 16:03:07.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-01-17 16:03:07.310][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-01-17 16:03:07.312][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-17 16:03:07.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-17 16:03:07.313][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-01-17 16:03:07.313][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-01-17 16:03:07.314][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-17 16:03:07.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:07.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:07.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-17 16:03:07.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-17 16:03:07.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-17 16:03:07.324][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-17 16:03:07.326][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-01-17 16:03:07.326][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-01-17 16:03:07.328][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-17 16:03:07.330][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-17 16:03:07.331][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-17 16:03:07.333][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-17 16:03:07.344][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-01-17 16:03:07.346][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-17 16:03:07.349][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-17 16:03:07.351][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-17 16:03:07.353][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-17 16:03:07.380][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-01-17 16:03:07.397][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-01-17 16:03:07.408][biodb::testThat]
biodb.INFO [2026-01-17 16:03:07.409][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-17 16:03:07.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:07.411][biodb::testThat]
biodb.TRACE[2026-01-17 16:03:07.416][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[2026-01-17 16:03:07.418][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-01-17 16:03:07.422][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-01-17 16:03:07.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-17 16:03:07.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:07.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:07.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:07.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:07.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:07.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-17 16:03:07.464][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:07.466][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:07.467][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.468][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:07.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:07.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.501][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:07.502][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:07.503][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.504][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.540][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:07.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:07.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.545][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.546][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.547][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.548][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.550][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.555][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.556][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.558][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.559][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.560][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.565][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.567][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.568][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.569][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.576][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.577][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.578][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.579][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.586][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.587][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.588][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.589][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.591][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.596][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.597][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.598][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.600][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.606][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.608][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.609][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.610][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.616][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.618][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.619][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.620][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.622][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.627][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:07.628][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:07.629][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.630][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.632][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:07.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:07.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.637][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:07.638][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:07.639][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.640][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:07.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:07.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.647][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.648][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.650][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.651][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.652][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.657][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.659][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.660][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.661][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.668][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:07.669][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:07.670][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.671][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:07.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:07.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.678][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:07.679][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:07.680][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.681][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.683][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:07.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:07.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.692][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:07.693][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:07.694][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.695][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.697][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:07.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:07.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.702][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-01-17 16:03:07.703][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:07.704][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.706][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.707][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-01-17 16:03:07.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:07.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:07.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:07.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:07.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:07.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:07.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:07.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.774][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.779][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.784][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:07.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.789][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.794][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.799][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:07.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:07.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:07.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.833][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.838][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.843][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:07.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.848][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.853][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:07.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:07.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:07.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.868][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:07.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:07.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.873][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:07.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:07.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.878][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:07.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:07.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.883][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:07.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:07.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.888][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:07.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:07.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.893][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:07.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:07.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.902][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:07.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:07.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:07.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:07.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.911][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:07.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:07.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:07.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:07.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.921][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:07.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:07.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.931][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:07.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.941][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.946][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.951][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:07.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:07.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:07.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:07.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:07.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:07.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:07.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:07.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.986][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.991][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:07.996][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:07.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:07.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.001][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.005][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.010][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.015][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:08.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:08.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.020][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:08.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:08.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:08.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:08.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.030][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-17 16:03:08.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.051][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-17 16:03:08.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.138][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.143][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.153][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-17 16:03:08.188][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-01-17 16:03:08.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-17 16:03:08.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-17 16:03:08.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.196][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-17 16:03:08.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-17 16:03:08.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.200][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-17 16:03:08.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-17 16:03:08.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.205][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-17 16:03:08.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-17 16:03:08.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.263][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.308][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.313][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.318][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-17 16:03:08.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.348][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.349][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.350][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.352][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:08.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.369][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.374][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.379][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.384][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.386][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.387][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.388][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.389][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:08.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.424][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.426][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.427][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.428][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:08.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.445][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.450][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.455][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.460][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.461][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.463][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.464][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.465][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:08.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.497][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.498][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.499][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.501][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:08.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.518][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.523][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.528][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.533][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.534][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.535][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.536][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.538][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:08.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.568][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.569][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.571][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.572][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:08.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:08.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.588][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:08.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:08.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.594][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:08.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.599][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:08.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:08.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.604][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:08.605][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:08.606][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.608][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.609][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:08.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:08.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.630][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:08.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:08.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:08.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:08.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.640][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:08.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:08.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.645][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:08.646][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:08.647][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.649][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:08.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:08.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.671][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.676][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.681][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.683][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.684][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.685][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.686][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:08.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.717][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.719][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.720][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.721][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:08.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.740][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.745][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.750][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.756][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.757][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.758][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.759][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.761][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:08.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.776][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.782][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.792][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.793][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.794][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.796][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.797][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:08.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.813][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.818][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.823][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.828][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.830][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.831][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.832][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.833][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:08.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.853][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:08.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:08.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.859][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:08.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:08.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.864][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:08.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:08.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.869][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:08.870][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:08.871][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.873][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.874][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:08.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:08.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:08.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:08.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:08.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:08.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:08.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:08.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.904][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:08.906][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:08.907][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.908][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:08.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:08.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.940][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.942][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.943][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.944][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.945][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:08.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.961][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.967][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.972][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.977][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.978][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.979][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.980][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.982][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:08.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:08.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:08.997][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-17 16:03:08.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-17 16:03:09.001][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.002][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.008][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-17 16:03:09.010][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-17 16:03:09.011][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.012][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.019][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-17 16:03:09.020][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-17 16:03:09.021][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.023][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.029][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-17 16:03:09.031][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-17 16:03:09.032][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.033][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.040][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:09.041][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-17 16:03:09.042][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.044][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.050][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:09.051][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-17 16:03:09.053][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.054][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.060][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:09.062][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-17 16:03:09.063][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.064][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.071][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:09.072][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-17 16:03:09.073][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.074][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.085][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:09.087][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:09.088][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.089][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.095][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-17 16:03:09.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-17 16:03:09.098][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.099][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.106][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-17 16:03:09.107][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-17 16:03:09.108][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.110][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.116][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-17 16:03:09.117][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-17 16:03:09.119][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.120][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.126][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:09.128][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-17 16:03:09.129][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.130][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.137][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:09.138][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-17 16:03:09.139][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.141][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.147][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:09.149][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:09.150][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.151][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.158][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:09.159][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-17 16:03:09.160][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.161][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.168][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:09.169][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:09.171][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.172][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:09.178][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-17 16:03:09.180][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-17 16:03:09.181][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.182][ef$get] fields variable is a list.
biodb.INFO [2026-01-17 16:03:09.192][biodb::testThat]
biodb.INFO [2026-01-17 16:03:09.194][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-17 16:03:09.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:09.196][biodb::testThat]
biodb.DEBUG[2026-01-17 16:03:09.215][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-17 16:03:09.219][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-17 16:03:09.222][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-17 16:03:09.263][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-17 16:03:09.265][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-17 16:03:09.266][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-17 16:03:09.443][biodb::testThat]
biodb.INFO [2026-01-17 16:03:09.445][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-17 16:03:09.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:09.447][biodb::testThat]
biodb.TRACE[2026-01-17 16:03:09.451][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:09.453][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:09.454][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:09.455][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-17 16:03:09.457][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-01-17 16:03:09.487][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-17 16:03:09.560][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-17 16:03:09.562][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-17 16:03:09.563][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-17 16:03:09.565][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-17 16:03:09.582][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-17 16:03:09.655][biodb::testThat]
biodb.INFO [2026-01-17 16:03:09.657][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-17 16:03:09.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:09.659][biodb::testThat]
biodb.DEBUG[2026-01-17 16:03:09.669][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-17 16:03:09.670][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-17 16:03:09.672][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-17 16:03:09.673][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-17 16:03:09.675][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-17 16:03:09.676][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-17 16:03:09.737][biodb::testThat]
biodb.INFO [2026-01-17 16:03:09.738][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-17 16:03:09.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:09.741][biodb::testThat]
biodb.DEBUG[2026-01-17 16:03:09.746][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-17 16:03:09.747][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-17 16:03:09.749][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-17 16:03:09.750][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-17 16:03:09.752][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-17 16:03:09.753][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-17 16:03:09.810][biodb::testThat]
biodb.INFO [2026-01-17 16:03:09.811][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-17 16:03:09.813][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:09.814][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-17 16:03:09.877][biodb::testThat]
biodb.INFO [2026-01-17 16:03:09.879][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-17 16:03:09.880][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:09.881][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-17 16:03:09.940][biodb::testThat]
biodb.INFO [2026-01-17 16:03:09.941][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-17 16:03:09.942][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:09.943][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-17 16:03:10.003][biodb::testThat]
biodb.INFO [2026-01-17 16:03:10.004][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-17 16:03:10.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-17 16:03:10.006][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-01-17 16:03:10.090][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:10.091][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:10.093][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:10.094][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:10.095][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:10.096][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:10.098][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:10.099][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:10.100][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:10.101][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:10.103][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:10.104][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:10.105][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-17 16:03:10.107][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-17 16:03:10.108][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:10.109][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:10.110][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-17 16:03:10.111][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-17 16:03:10.113][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:10.114][ef$get] fields variable is a list.
biodb.TRACE[2026-01-17 16:03:10.115][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:10.116][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-17 16:03:10.118][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-17 16:03:10.119][ef$get] fields variable is a list.
biodb.INFO [2026-01-17 16:03:10.120][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-17 16:03:10.121][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-01-17 16:03:10.123][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-17 16:03:10.124][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-17 16:03:10.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-17 16:03:10.126][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-17 16:03:10.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-17 16:03:10.128][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-17 16:03:10.129][FUN] Functions in observer 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)