Back to Long Tests report for BioC 3.22

This page was generated on 2026-03-07 23:55 -0500 (Sat, 07 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4892
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4684
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: 2026-03-07 09:55 -0500 (Sat, 07 Mar 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: 2026-03-07 16:01:50 -0500 (Sat, 07 Mar 2026)
EndedAt: 2026-03-07 16:03:20 -0500 (Sat, 07 Mar 2026)
EllapsedTime: 89.6 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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> # 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 [2026-03-07 16:03:15.776][biodb::testContext]
biodb.INFO [2026-03-07 16:03:15.780][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:03:15.781][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-03-07 16:03:15.783][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-07 16:03:15.784][biodb::testContext]
biodb.INFO [2026-03-07 16:03:15.790][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:03:15.792][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-07 16:03:15.800][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:15.801][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-07 16:03:15.803][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-07 16:03:15.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.807][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-07 16:03:15.832][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-07 16:03:15.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.835][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:15.836][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-07 16:03:15.838][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-07 16:03:15.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.842][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-07 16:03:15.844][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-07 16:03:15.845][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-07 16:03:15.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.848][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:15.850][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-07 16:03:15.851][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-07 16:03:15.852][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-07 16:03:15.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.857][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-07 16:03:15.858][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-07 16:03:15.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.863][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-07 16:03:15.864][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-07 16:03:15.865][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-07 16:03:15.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.870][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-07 16:03:15.871][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-07 16:03:15.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.876][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-07 16:03:15.878][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-07 16:03:15.879][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-07 16:03:15.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.884][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:03:15.885][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-07 16:03:15.886][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-07 16:03:15.888][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-07 16:03:15.889][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-07 16:03:15.890][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-07 16:03:15.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.894][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:15.895][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-07 16:03:15.896][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-07 16:03:15.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.901][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-07 16:03:15.902][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-07 16:03:15.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.906][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:15.907][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-07 16:03:15.909][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-07 16:03:15.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.914][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-07 16:03:15.915][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-07 16:03:15.916][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-07 16:03:15.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.921][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-07 16:03:15.922][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-07 16:03:15.933][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-07 16:03:15.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.938][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-07 16:03:15.939][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-07 16:03:15.941][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-07 16:03:15.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:15.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:15.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:15.948][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-07 16:03:15.991][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.019][self$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[2026-03-07 16:03:16.020][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.022][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:16.023][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.024][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.025][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.027][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.028][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:03:16.029][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:16.030][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.032][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-07 16:03:16.033][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:16.034][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.037][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:03:16.037][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:03:16.037][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:03:16.037][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:03:16.037][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:03:16.038][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:16.039][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.042][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:16.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.045][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.046][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.048][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:16.049][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:16.050][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.051][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.053][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-07 16:03:16.055][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.056][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:03:16.057][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.059][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:16.060][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.064][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.065][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:03:16.066][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:16.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.069][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-07 16:03:16.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:16.071][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.072][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.074][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:03:16.074][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-07 16:03:16.074][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-07 16:03:16.074][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-07 16:03:16.074][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-07 16:03:16.075][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:16.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.079][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:16.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.082][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.083][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.085][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:16.086][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:16.087][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.088][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.090][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-07 16:03:16.092][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.093][self$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[2026-03-07 16:03:16.094][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.096][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:16.097][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.098][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.100][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.101][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.102][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-07 16:03:16.103][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:16.105][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.106][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-07 16:03:16.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:16.109][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.110][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.111][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.112][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:16.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.116][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:16.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.121][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.122][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:16.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:16.124][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.126][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.127][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-07 16:03:16.129][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.130][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-07 16:03:16.132][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:16.134][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.135][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.137][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.138][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.139][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-07 16:03:16.140][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:16.142][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.143][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-07 16:03:16.144][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:16.145][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.147][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.148][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.149][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-07 16:03:16.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.153][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:16.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.155][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.156][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.158][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.159][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:16.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:16.161][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.162][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.167][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:16.168][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.174][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.186][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.191][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.197][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.203][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.220][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.225][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.242][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.248][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.253][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.259][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.260][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-07 16:03:16.265][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-07 16:03:16.267][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-07 16:03:16.273][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-07 16:03:16.275][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-07 16:03:16.276][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:03:16.278][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-07 16:03:16.280][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-07 16:03:16.281][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-07 16:03:16.283][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:03:16.285][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:03:16.286][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-07 16:03:16.288][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-07 16:03:16.290][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-07 16:03:16.291][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-07 16:03:16.293][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:03:16.295][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-07 16:03:16.297][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-07 16:03:16.299][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-07 16:03:16.301][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-07 16:03:16.302][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-07 16:03:16.304][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-07 16:03:16.306][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-07 16:03:16.308][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-07 16:03:16.310][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-07 16:03:16.312][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-07 16:03:16.314][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-07 16:03:16.316][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-07 16:03:16.318][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-07 16:03:16.319][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-07 16:03:16.321][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-07 16:03:16.323][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-07 16:03:16.325][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-07 16:03:16.326][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-07 16:03:16.328][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-07 16:03:16.330][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-07 16:03:16.331][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-07 16:03:16.333][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-07 16:03:16.335][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-07 16:03:16.337][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-07 16:03:16.338][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-07 16:03:16.340][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-07 16:03:16.342][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-07 16:03:16.344][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-07 16:03:16.345][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-07 16:03:16.347][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-07 16:03:16.349][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-07 16:03:16.350][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-07 16:03:16.352][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-07 16:03:16.354][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-07 16:03:16.356][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-07 16:03:16.357][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-07 16:03:16.359][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-07 16:03:16.361][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-07 16:03:16.363][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-07 16:03:16.364][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-07 16:03:16.366][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-07 16:03:16.368][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-07 16:03:16.370][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-07 16:03:16.371][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-07 16:03:16.373][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-07 16:03:16.375][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-07 16:03:16.377][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-07 16:03:16.378][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-07 16:03:16.380][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-07 16:03:16.382][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-07 16:03:16.384][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-07 16:03:16.385][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-07 16:03:16.387][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-07 16:03:16.389][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-07 16:03:16.391][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-07 16:03:16.393][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-07 16:03:16.395][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-07 16:03:16.396][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-07 16:03:16.398][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-07 16:03:16.400][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-07 16:03:16.402][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-07 16:03:16.403][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-07 16:03:16.405][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-07 16:03:16.407][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-07 16:03:16.408][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-07 16:03:16.410][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-07 16:03:16.412][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-07 16:03:16.419][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-07 16:03:16.421][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-07 16:03:16.425][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-07 16:03:16.426][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.428][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.442][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.450][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[2026-03-07 16:03:16.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.457][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.465][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.473][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.481][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.489][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[2026-03-07 16:03:16.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.513][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.541][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-07 16:03:16.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.557][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2026-03-07 16:03:16.566][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-03-07 16:03:16.578][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-03-07 16:03:16.601][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-03-07 16:03:16.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-07 16:03:16.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.609][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.612][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-03-07 16:03:16.625][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-03-07 16:03:16.627][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.629][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.630][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.631][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-07 16:03:16.633][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.634][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-03-07 16:03:16.635][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.636][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.638][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-07 16:03:16.639][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-07 16:03:16.640][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.641][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-03-07 16:03:16.643][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-03-07 16:03:16.644][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-03-07 16:03:16.646][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-07 16:03:16.647][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-07 16:03:16.647][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-03-07 16:03:16.647][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-03-07 16:03:16.648][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-07 16:03:16.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.652][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-07 16:03:16.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-07 16:03:16.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-07 16:03:16.655][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-07 16:03:16.657][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-03-07 16:03:16.657][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-03-07 16:03:16.658][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-07 16:03:16.659][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-07 16:03:16.660][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-07 16:03:16.662][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-07 16:03:16.670][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-03-07 16:03:16.672][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-07 16:03:16.674][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-07 16:03:16.676][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-07 16:03:16.678][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-07 16:03:16.699][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-03-07 16:03:16.715][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-03-07 16:03:16.725][biodb::testThat]
biodb.INFO [2026-03-07 16:03:16.727][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-07 16:03:16.728][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:16.729][biodb::testThat]
biodb.TRACE[2026-03-07 16:03:16.734][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[2026-03-07 16:03:16.736][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-03-07 16:03:16.740][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-03-07 16:03:16.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-07 16:03:16.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:16.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:16.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:16.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:16.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:16.771][FUN] Functions in observer BiodbConfig: [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[2026-03-07 16:03:16.782][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:16.784][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:16.785][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.786][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:16.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:16.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.820][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:16.821][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:16.822][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.823][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.859][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:16.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:16.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.864][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:16.865][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:16.866][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.868][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.869][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:16.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:16.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.874][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:16.876][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:16.877][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.878][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.879][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:16.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:16.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.885][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:16.886][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:16.887][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.888][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:16.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:16.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.895][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:16.896][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:16.897][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.899][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:16.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:16.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.905][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:16.907][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:16.908][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.909][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.911][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:16.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:16.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.916][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:16.917][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:16.918][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.919][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.921][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:16.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:16.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.926][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:16.927][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:16.929][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.930][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.931][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:16.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:16.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.936][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:16.938][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:16.939][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.940][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.941][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.946][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:16.948][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:16.949][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.950][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:16.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:16.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.956][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:16.958][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:16.959][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.960][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:16.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:16.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.967][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:16.968][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:16.969][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.970][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:16.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:16.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.977][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:16.978][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:16.979][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.980][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:16.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:16.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.987][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:16.988][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:16.990][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.991][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:16.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:16.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:16.997][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:16.998][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.000][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.001][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.002][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.007][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:17.009][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:17.010][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.011][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.012][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:17.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:17.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.017][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-03-07 16:03:17.019][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:17.020][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.021][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.023][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-03-07 16:03:17.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:17.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.089][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.094][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.099][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.104][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:17.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:17.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.109][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:17.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:17.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.114][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:17.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:17.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.148][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:17.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:17.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.153][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:17.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:17.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.158][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:17.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:17.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:17.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:17.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:17.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:17.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.173][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:17.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:17.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.178][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:17.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:17.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.183][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:17.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:17.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.188][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:17.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:17.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.193][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.198][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.202][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.207][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:17.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:17.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.212][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:17.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:17.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.217][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:17.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:17.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:17.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:17.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:17.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:17.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:17.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:17.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.255][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.260][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.265][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.299][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.304][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.309][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.314][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.324][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.329][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:17.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:17.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.334][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:17.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:17.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.339][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:17.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:17.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.344][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-03-07 16:03:17.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.364][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-03-07 16:03:17.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:17.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.407][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.417][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.422][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.432][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:03:17.499][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-03-07 16:03:17.502][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:03:17.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:03:17.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.507][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-07 16:03:17.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-07 16:03:17.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.512][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-07 16:03:17.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-07 16:03:17.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.517][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-07 16:03:17.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-07 16:03:17.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.534][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.576][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.581][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.586][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-07 16:03:17.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.615][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.616][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.618][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.619][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:17.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:17.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.641][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.646][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.651][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.652][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.653][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.655][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.656][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:17.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.686][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.688][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.689][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.690][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:17.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.712][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.717][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.727][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.728][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.729][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.730][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.763][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.765][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.766][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.767][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:17.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.784][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.790][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.795][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.800][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.801][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.802][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.804][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.805][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:17.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.841][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.844][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.845][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:17.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:17.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.862][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.867][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.872][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.878][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.879][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.880][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.881][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.883][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:17.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:17.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.899][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:17.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:17.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:17.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:17.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.909][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:17.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:17.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.915][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:17.916][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:17.917][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.919][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:17.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:17.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.945][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.950][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.955][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.956][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.957][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.958][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.960][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:17.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.975][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.991][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.992][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.993][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.994][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:17.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:17.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:17.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.027][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.032][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.033][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.035][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.036][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.037][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.068][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.070][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.071][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.072][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.073][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.094][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.100][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.105][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.106][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.107][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.109][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.110][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.126][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:18.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:18.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.131][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:18.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.136][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:18.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:18.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.141][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:18.142][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:18.144][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.145][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.146][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:18.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:18.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:18.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:18.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:18.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:18.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:18.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.183][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:18.184][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:18.185][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.186][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:18.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:18.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.209][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.219][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.220][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.221][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.222][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.239][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.245][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.250][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.255][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.256][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.258][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.259][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.260][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.276][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-07 16:03:18.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-07 16:03:18.279][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.280][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.287][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-07 16:03:18.289][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-07 16:03:18.290][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.291][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.298][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.299][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-07 16:03:18.301][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.302][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.309][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-07 16:03:18.310][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-07 16:03:18.311][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.312][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.319][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:18.321][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-07 16:03:18.322][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.323][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.330][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.332][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-07 16:03:18.333][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.335][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.341][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.343][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-07 16:03:18.344][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.345][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.353][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.354][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-07 16:03:18.355][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.357][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.363][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:18.365][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:18.366][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.367][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.374][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-07 16:03:18.375][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-07 16:03:18.376][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.378][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.384][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-07 16:03:18.386][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-07 16:03:18.387][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.388][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.395][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.396][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-07 16:03:18.397][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.399][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.410][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:18.411][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-07 16:03:18.412][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.414][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.420][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:18.422][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-07 16:03:18.423][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.424][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.431][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:18.432][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:18.434][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.435][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.442][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:18.443][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-07 16:03:18.444][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.446][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.452][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:18.455][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:18.456][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.457][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:18.464][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-07 16:03:18.465][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-07 16:03:18.466][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.468][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:03:18.478][biodb::testThat]
biodb.INFO [2026-03-07 16:03:18.480][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-07 16:03:18.481][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:18.482][biodb::testThat]
biodb.DEBUG[2026-03-07 16:03:18.502][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-07 16:03:18.507][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:03:18.510][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-07 16:03:18.551][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-07 16:03:18.553][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-07 16:03:18.554][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:03:18.733][biodb::testThat]
biodb.INFO [2026-03-07 16:03:18.734][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-07 16:03:18.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:18.737][biodb::testThat]
biodb.TRACE[2026-03-07 16:03:18.741][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:18.742][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:18.743][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:18.745][ef$get] fields variable is a list.
biodb.DEBUG[2026-03-07 16:03:18.746][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-03-07 16:03:18.777][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-07 16:03:18.846][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:03:18.848][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-07 16:03:18.850][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-07 16:03:18.852][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-07 16:03:18.869][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:03:18.942][biodb::testThat]
biodb.INFO [2026-03-07 16:03:18.944][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-07 16:03:18.945][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:18.946][biodb::testThat]
biodb.DEBUG[2026-03-07 16:03:18.957][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-07 16:03:18.958][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:03:18.960][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-07 16:03:18.962][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-07 16:03:18.964][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-07 16:03:18.965][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:03:19.027][biodb::testThat]
biodb.INFO [2026-03-07 16:03:19.028][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-07 16:03:19.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:19.031][biodb::testThat]
biodb.DEBUG[2026-03-07 16:03:19.036][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-07 16:03:19.037][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-07 16:03:19.039][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-07 16:03:19.041][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-07 16:03:19.042][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-07 16:03:19.043][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:03:19.101][biodb::testThat]
biodb.INFO [2026-03-07 16:03:19.102][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-07 16:03:19.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:19.104][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:03:19.164][biodb::testThat]
biodb.INFO [2026-03-07 16:03:19.165][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-07 16:03:19.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:19.168][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:03:19.230][biodb::testThat]
biodb.INFO [2026-03-07 16:03:19.232][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-07 16:03:19.233][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:19.234][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-07 16:03:19.291][biodb::testThat]
biodb.INFO [2026-03-07 16:03:19.293][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-07 16:03:19.294][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-07 16:03:19.295][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-03-07 16:03:19.375][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:19.376][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:19.377][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:19.379][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:19.380][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:19.381][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:19.382][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:19.383][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:19.385][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:19.386][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:19.387][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:19.388][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:19.390][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-07 16:03:19.391][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-07 16:03:19.392][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:19.393][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:19.394][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-07 16:03:19.396][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-07 16:03:19.397][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:19.398][ef$get] fields variable is a list.
biodb.TRACE[2026-03-07 16:03:19.399][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:19.400][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-07 16:03:19.402][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-07 16:03:19.403][ef$get] fields variable is a list.
biodb.INFO [2026-03-07 16:03:19.404][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-07 16:03:19.405][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-03-07 16:03:19.406][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-07 16:03:19.408][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-07 16:03:19.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-07 16:03:19.410][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-07 16:03:19.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-07 16:03:19.412][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-07 16:03:19.413][FUN] Functions in observer 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)