Back to Long Tests report for BioC 3.22

This page was generated on 2026-01-03 23:55 -0500 (Sat, 03 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
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: 2026-01-03 09:55 -0500 (Sat, 03 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: 2026-01-03 16:01:34 -0500 (Sat, 03 Jan 2026)
EndedAt: 2026-01-03 16:03:03 -0500 (Sat, 03 Jan 2026)
EllapsedTime: 88.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2026-01-03 16:02:58.001][biodb::testContext]
biodb.INFO [2026-01-03 16:02:58.005][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-03 16:02:58.007][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-01-03 16:02:58.008][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-03 16:02:58.009][biodb::testContext]
biodb.INFO [2026-01-03 16:02:58.016][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-03 16:02:58.018][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-03 16:02:58.026][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-03 16:02:58.028][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-03 16:02:58.029][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-03 16:02:58.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.034][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-03 16:02:58.060][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-03 16:02:58.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.064][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.065][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-03 16:02:58.066][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-03 16:02:58.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.082][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-03 16:02:58.083][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-03 16:02:58.085][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-03 16:02:58.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.088][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.089][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-03 16:02:58.090][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-03 16:02:58.092][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-03 16:02:58.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.096][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-03 16:02:58.098][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-03 16:02:58.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.101][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.102][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-03 16:02:58.104][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-03 16:02:58.105][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-03 16:02:58.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.110][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-03 16:02:58.111][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-03 16:02:58.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.114][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.115][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-03 16:02:58.117][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-03 16:02:58.118][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-03 16:02:58.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.123][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-03 16:02:58.124][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-03 16:02:58.125][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-03 16:02:58.127][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-03 16:02:58.128][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-03 16:02:58.129][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-03 16:02:58.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.133][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[2026-01-03 16:02:58.134][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-03 16:02:58.136][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-03 16:02:58.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.140][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-03 16:02:58.142][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-03 16:02:58.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.145][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.146][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-03 16:02:58.148][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-03 16:02:58.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.152][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-03 16:02:58.154][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-03 16:02:58.155][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-03 16:02:58.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.158][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.160][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-03 16:02:58.161][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-03 16:02:58.172][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-03 16:02:58.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.178][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-03 16:02:58.179][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-03 16:02:58.180][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-03 16:02:58.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.184][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.188][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-03 16:02:58.232][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.254][self$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[2026-01-03 16:02:58.255][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-03 16:02:58.258][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.262][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.263][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-03 16:02:58.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-03 16:02:58.265][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.267][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-03 16:02:58.268][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-03 16:02:58.269][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.270][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.272][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-03 16:02:58.272][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-03 16:02:58.272][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-03 16:02:58.272][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-03 16:02:58.272][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-03 16:02:58.273][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-03 16:02:58.274][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.275][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.276][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-03 16:02:58.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.280][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.281][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.282][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-03 16:02:58.284][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-03 16:02:58.285][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.286][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.287][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-03 16:02:58.290][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.291][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-03 16:02:58.292][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.293][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-03 16:02:58.295][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.296][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.297][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.298][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.300][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-03 16:02:58.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-03 16:02:58.307][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.308][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-03 16:02:58.309][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-03 16:02:58.311][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.312][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-03 16:02:58.313][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-03 16:02:58.313][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-03 16:02:58.313][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-03 16:02:58.313][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-03 16:02:58.315][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-03 16:02:58.316][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.317][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.318][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-03 16:02:58.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.322][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.323][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.325][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-03 16:02:58.326][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-03 16:02:58.327][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.328][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.330][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-03 16:02:58.332][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.333][self$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[2026-01-03 16:02:58.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.336][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-03 16:02:58.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.340][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.342][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.343][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-03 16:02:58.345][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-03 16:02:58.346][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.347][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-03 16:02:58.348][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-03 16:02:58.350][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.351][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.352][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.354][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-03 16:02:58.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.357][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-03 16:02:58.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.361][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.362][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.363][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-03 16:02:58.364][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-03 16:02:58.365][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.367][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.368][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-03 16:02:58.370][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.372][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-03 16:02:58.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-03 16:02:58.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.377][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.378][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.379][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.381][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-03 16:02:58.382][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-03 16:02:58.383][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.384][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-03 16:02:58.386][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-03 16:02:58.387][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.388][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.389][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.391][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-03 16:02:58.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.394][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-03 16:02:58.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.398][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.399][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.400][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-03 16:02:58.401][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-03 16:02:58.403][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.404][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.408][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-03 16:02:58.409][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.410][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.421][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.427][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.444][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.461][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.467][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.472][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.484][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.489][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.495][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.502][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-03 16:02:58.507][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-03 16:02:58.509][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-03 16:02:58.510][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-03 16:02:58.512][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-03 16:02:58.514][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-03 16:02:58.516][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-03 16:02:58.522][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-03 16:02:58.524][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-03 16:02:58.526][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-03 16:02:58.528][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-03 16:02:58.530][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-03 16:02:58.532][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-03 16:02:58.534][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-03 16:02:58.536][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-03 16:02:58.538][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-03 16:02:58.539][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-03 16:02:58.541][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-03 16:02:58.543][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-03 16:02:58.545][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-03 16:02:58.547][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-03 16:02:58.549][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-03 16:02:58.551][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-03 16:02:58.553][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-03 16:02:58.555][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-03 16:02:58.557][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-03 16:02:58.559][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-03 16:02:58.561][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-03 16:02:58.563][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-03 16:02:58.565][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-03 16:02:58.567][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-03 16:02:58.569][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-03 16:02:58.571][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-03 16:02:58.573][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-03 16:02:58.575][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-03 16:02:58.577][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-03 16:02:58.578][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-03 16:02:58.580][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-03 16:02:58.582][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-03 16:02:58.584][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-03 16:02:58.585][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-03 16:02:58.587][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-03 16:02:58.589][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-03 16:02:58.591][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-03 16:02:58.592][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-03 16:02:58.594][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-03 16:02:58.596][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-03 16:02:58.598][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-03 16:02:58.600][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-03 16:02:58.601][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-03 16:02:58.603][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-03 16:02:58.605][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-03 16:02:58.606][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-03 16:02:58.608][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-03 16:02:58.610][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-03 16:02:58.612][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-03 16:02:58.613][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-03 16:02:58.615][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-03 16:02:58.617][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-03 16:02:58.619][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-03 16:02:58.621][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-03 16:02:58.623][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-03 16:02:58.624][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-03 16:02:58.626][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-03 16:02:58.628][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-03 16:02:58.630][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-03 16:02:58.632][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-03 16:02:58.633][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-03 16:02:58.635][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-03 16:02:58.637][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-03 16:02:58.638][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-03 16:02:58.640][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-03 16:02:58.642][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-03 16:02:58.644][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-03 16:02:58.645][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-03 16:02:58.647][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-03 16:02:58.649][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-03 16:02:58.650][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-03 16:02:58.652][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-03 16:02:58.654][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-03 16:02:58.656][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-03 16:02:58.657][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-03 16:02:58.659][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-03 16:02:58.666][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-03 16:02:58.668][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-03 16:02:58.672][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-03 16:02:58.673][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.675][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.713][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.721][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.749][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.757][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.764][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.772][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.780][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.790][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.799][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.807][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:58.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.815][FUN] Functions in observer BiodbConfig: [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 [2026-01-03 16:02:58.817][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-01-03 16:02:58.828][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-01-03 16:02:58.848][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-01-03 16:02:58.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-03 16:02:58.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:58.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:58.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:58.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:58.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:58.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-03 16:02:58.859][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-01-03 16:02:58.872][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-01-03 16:02:58.875][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.876][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.878][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.879][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-03 16:02:58.880][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.881][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-01-03 16:02:58.883][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.884][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.885][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-03 16:02:58.887][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-03 16:02:58.888][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.889][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-01-03 16:02:58.890][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-01-03 16:02:58.892][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-01-03 16:02:58.893][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-03 16:02:58.895][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-03 16:02:58.895][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-01-03 16:02:58.895][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-01-03 16:02:58.896][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-03 16:02:58.897][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.900][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-03 16:02:58.901][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-03 16:02:58.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-03 16:02:58.903][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-03 16:02:58.905][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-01-03 16:02:58.905][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-01-03 16:02:58.906][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-03 16:02:58.907][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-03 16:02:58.908][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-03 16:02:58.909][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-03 16:02:58.917][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-01-03 16:02:58.919][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-03 16:02:58.922][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-03 16:02:58.924][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-03 16:02:58.926][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-03 16:02:58.952][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-01-03 16:02:58.968][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-01-03 16:02:58.977][biodb::testThat]
biodb.INFO [2026-01-03 16:02:58.978][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-03 16:02:58.980][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:02:58.981][biodb::testThat]
biodb.TRACE[2026-01-03 16:02:58.985][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[2026-01-03 16:02:58.987][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-01-03 16:02:58.991][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-01-03 16:02:58.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-03 16:02:59.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:02:59.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:02:59.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:02:59.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:02:59.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:02:59.020][FUN] Functions in observer BiodbConfig: [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[2026-01-03 16:02:59.031][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.033][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.034][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.035][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.059][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.060][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.061][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.062][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.099][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.104][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.106][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.107][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.108][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.110][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.115][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.117][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.118][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.119][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.121][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.127][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.129][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.130][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.137][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.138][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.139][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.141][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.159][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.161][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.162][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.163][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.165][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.170][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.172][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.175][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.177][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.179][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.186][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.188][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.189][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.190][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.192][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.200][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.202][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.204][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.206][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.209][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.216][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:02:59.218][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:02:59.220][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.221][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.223][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:02:59.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:02:59.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.228][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:02:59.230][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:02:59.231][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.232][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:02:59.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:02:59.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.239][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.241][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.242][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.243][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.250][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.253][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.254][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.263][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.266][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.268][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.269][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.276][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:02:59.278][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:02:59.279][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.280][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.282][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:02:59.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:02:59.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.291][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:02:59.293][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:02:59.295][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.297][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:02:59.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:02:59.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.304][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-01-03 16:02:59.306][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:02:59.307][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.308][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.310][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-01-03 16:02:59.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:02:59.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.427][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.432][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.438][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:02:59.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.447][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.455][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:02:59.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:02:59.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:02:59.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.524][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:02:59.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.530][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.535][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:02:59.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:02:59.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:02:59.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:02:59.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:02:59.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:02:59.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:02:59.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.561][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:02:59.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:02:59.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.566][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:02:59.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:02:59.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.571][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:02:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:02:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.576][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:02:59.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:02:59.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.582][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:02:59.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:02:59.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:02:59.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:02:59.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.597][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:02:59.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:02:59.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:02:59.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:02:59.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:02:59.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:02:59.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.613][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.628][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.633][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.639][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:02:59.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:02:59.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.659][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.674][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.679][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:02:59.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.689][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.694][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:02:59.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.704][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:02:59.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:02:59.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.710][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:02:59.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:02:59.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.715][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:02:59.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:02:59.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.720][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-03 16:02:59.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.740][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-03 16:02:59.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:02:59.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:02:59.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:02:59.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.826][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:02:59.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:02:59.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.834][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:02:59.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:02:59.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.846][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:02:59.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:02:59.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-03 16:02:59.890][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-01-03 16:02:59.895][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-03 16:02:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-03 16:02:59.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.904][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-03 16:02:59.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-03 16:02:59.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.914][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-03 16:02:59.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-03 16:02:59.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.924][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-03 16:02:59.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-03 16:02:59.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.949][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:02:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:02:59.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:02:59.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:02:59.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:02:59.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:02:59.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:03:00.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:03:00.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.010][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:03:00.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:03:00.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.016][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:03:00.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:03:00.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.023][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:03:00.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-03 16:03:00.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:03:00.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:03:00.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:03:00.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:03:00.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:03:00.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:03:00.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.067][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:03:00.070][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:03:00.072][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.074][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:03:00.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:03:00.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.103][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.111][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.120][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.130][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.131][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.132][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.134][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.135][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.168][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.169][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.171][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.172][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.191][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.199][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.209][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.218][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.219][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.221][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.222][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.223][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.258][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.260][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.261][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.262][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.279][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.284][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.289][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.294][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.295][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.297][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.298][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.299][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:00.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:00.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:00.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:00.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:00.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:00.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.330][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:00.331][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:00.332][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.333][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:00.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:00.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.350][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:03:00.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:03:00.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.356][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:03:00.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:03:00.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.361][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:03:00.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:03:00.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.366][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:03:00.367][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:03:00.368][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.370][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.371][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:03:00.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:03:00.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:03:00.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:03:00.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:03:00.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:03:00.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.402][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:03:00.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:03:00.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.408][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:03:00.409][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:03:00.410][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.411][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.413][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:03:00.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:03:00.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.434][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.440][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.445][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.446][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.448][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.449][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.450][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.483][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.484][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.485][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.487][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.504][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.515][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.520][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.521][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.522][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.524][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.525][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.541][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.546][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.551][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.556][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.557][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.559][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.560][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.581][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.586][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.591][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.596][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.598][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.599][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.600][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.601][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.617][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:03:00.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:03:00.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.622][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:03:00.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:03:00.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.629][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:03:00.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:03:00.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.634][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:03:00.636][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:03:00.638][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.640][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.643][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:03:00.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:03:00.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:03:00.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:03:00.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.678][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:03:00.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:03:00.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:03:00.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:03:00.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.695][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:03:00.698][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:03:00.700][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.702][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:03:00.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:03:00.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.753][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.755][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.757][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.758][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.783][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.789][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.794][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.803][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.804][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.805][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.807][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.808][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.823][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-03 16:03:00.825][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-03 16:03:00.826][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.827][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.834][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.835][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-03 16:03:00.836][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.838][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.844][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.846][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-03 16:03:00.847][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.848][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.855][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.856][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-03 16:03:00.858][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.859][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.865][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.867][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-03 16:03:00.868][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.869][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.876][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.878][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-03 16:03:00.879][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.880][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.887][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.888][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-03 16:03:00.889][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.891][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.897][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.899][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-03 16:03:00.900][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.901][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.908][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:03:00.909][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:03:00.911][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.912][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.918][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-03 16:03:00.920][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-03 16:03:00.921][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.922][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.929][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-03 16:03:00.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-03 16:03:00.932][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.933][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.939][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.941][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-03 16:03:00.942][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.943][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.950][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.951][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-03 16:03:00.952][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.954][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.960][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.961][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-03 16:03:00.963][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.964][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.970][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:00.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:00.973][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.974][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.981][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.986][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-03 16:03:00.987][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.989][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:00.995][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.997][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:00.998][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:00.999][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:01.005][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-03 16:03:01.007][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-03 16:03:01.008][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:01.009][ef$get] fields variable is a list.
biodb.INFO [2026-01-03 16:03:01.020][biodb::testThat]
biodb.INFO [2026-01-03 16:03:01.021][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-03 16:03:01.022][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:03:01.023][biodb::testThat]
biodb.DEBUG[2026-01-03 16:03:01.042][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-03 16:03:01.046][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-03 16:03:01.049][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-03 16:03:01.089][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-03 16:03:01.091][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-03 16:03:01.093][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-03 16:03:01.275][biodb::testThat]
biodb.INFO [2026-01-03 16:03:01.277][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-03 16:03:01.278][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:03:01.279][biodb::testThat]
biodb.TRACE[2026-01-03 16:03:01.283][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:01.285][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:01.286][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:01.292][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-03 16:03:01.294][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-01-03 16:03:01.324][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-03 16:03:01.389][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-03 16:03:01.391][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-03 16:03:01.393][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-03 16:03:01.394][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-03 16:03:01.412][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-03 16:03:01.492][biodb::testThat]
biodb.INFO [2026-01-03 16:03:01.493][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-03 16:03:01.494][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:03:01.495][biodb::testThat]
biodb.DEBUG[2026-01-03 16:03:01.505][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-03 16:03:01.507][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-03 16:03:01.508][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-03 16:03:01.510][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-03 16:03:01.512][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-03 16:03:01.513][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-03 16:03:01.576][biodb::testThat]
biodb.INFO [2026-01-03 16:03:01.577][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-03 16:03:01.578][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:03:01.579][biodb::testThat]
biodb.DEBUG[2026-01-03 16:03:01.584][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-03 16:03:01.586][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-03 16:03:01.587][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-03 16:03:01.589][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-03 16:03:01.591][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-03 16:03:01.592][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-03 16:03:01.650][biodb::testThat]
biodb.INFO [2026-01-03 16:03:01.651][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-03 16:03:01.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:03:01.653][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-03 16:03:01.717][biodb::testThat]
biodb.INFO [2026-01-03 16:03:01.718][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-03 16:03:01.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:03:01.721][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-03 16:03:01.782][biodb::testThat]
biodb.INFO [2026-01-03 16:03:01.783][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-03 16:03:01.784][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:03:01.785][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-03 16:03:01.851][biodb::testThat]
biodb.INFO [2026-01-03 16:03:01.853][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-03 16:03:01.854][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-03 16:03:01.855][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-01-03 16:03:01.933][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:01.935][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:01.936][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:01.937][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:01.938][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:03:01.940][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:03:01.941][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:01.942][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:01.943][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:01.945][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:01.946][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:01.947][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:01.949][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-03 16:03:01.950][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-03 16:03:01.951][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:01.953][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:01.954][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-03 16:03:01.955][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-03 16:03:01.956][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:01.958][ef$get] fields variable is a list.
biodb.TRACE[2026-01-03 16:03:01.959][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:01.960][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-03 16:03:01.961][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-03 16:03:01.963][ef$get] fields variable is a list.
biodb.INFO [2026-01-03 16:03:01.964][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-03 16:03:01.965][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-01-03 16:03:01.967][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-03 16:03:01.968][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-03 16:03:01.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-03 16:03:01.970][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-03 16:03:01.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-03 16:03:01.977][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-03 16:03:01.978][FUN] Functions in observer 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)