Back to Long Tests report for BioC 3.22

This page was generated on 2025-12-20 23:55 -0500 (Sat, 20 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-12-20 09:55 -0500 (Sat, 20 Dec 2025)
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 nebbiolo2

To the developers/maintainers of the biodbHmdb package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-12-20 16:01:11 -0500 (Sat, 20 Dec 2025)
EndedAt: 2025-12-20 16:02:20 -0500 (Sat, 20 Dec 2025)
EllapsedTime: 69.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-12-20 16:02:16.853][biodb::testContext]
biodb.INFO [2025-12-20 16:02:16.855][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:16.856][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-12-20 16:02:16.857][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:16.858][biodb::testContext]
biodb.INFO [2025-12-20 16:02:16.864][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:16.866][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:16.872][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:16.873][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-20 16:02:16.874][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-20 16:02:16.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.878][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-20 16:02:16.894][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-20 16:02:16.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.897][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:16.898][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-20 16:02:16.899][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-20 16:02:16.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.911][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-20 16:02:16.912][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-20 16:02:16.913][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-20 16:02:16.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.916][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-20 16:02:16.917][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-20 16:02:16.918][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-20 16:02:16.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.921][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-20 16:02:16.922][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-20 16:02:16.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.925][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:16.925][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-20 16:02:16.926][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-20 16:02:16.927][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-20 16:02:16.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.931][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-20 16:02:16.932][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-20 16:02:16.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.934][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:16.935][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-20 16:02:16.936][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-20 16:02:16.937][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-20 16:02:16.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.940][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:16.941][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-20 16:02:16.942][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-20 16:02:16.943][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-20 16:02:16.944][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-20 16:02:16.945][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-20 16:02:16.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.947][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:16.948][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-20 16:02:16.949][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-20 16:02:16.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.953][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-20 16:02:16.953][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-20 16:02:16.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.956][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:16.957][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-20 16:02:16.958][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-20 16:02:16.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.961][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-20 16:02:16.962][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-20 16:02:16.963][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-20 16:02:16.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.965][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:16.966][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:16.967][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-20 16:02:16.971][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-20 16:02:16.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:16.974][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-20 16:02:16.975][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-20 16:02:16.976][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-20 16:02:16.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:16.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:16.979][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:16.982][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-20 16:02:17.012][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.027][self$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[2025-12-20 16:02:17.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.029][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:17.030][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.031][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.032][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.033][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.033][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:17.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:17.035][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.036][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-20 16:02:17.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:17.038][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.039][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.040][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:17.040][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:17.040][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:17.040][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:17.040][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:17.041][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:17.042][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:17.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.045][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.046][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.047][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.048][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:17.049][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:17.050][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.050][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.052][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-20 16:02:17.053][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.054][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:17.055][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.056][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:17.057][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.058][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.059][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.064][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.065][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:17.066][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:17.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.067][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-20 16:02:17.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:17.069][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.070][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.071][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:17.071][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:17.071][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:17.071][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:17.071][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:17.072][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:17.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.075][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:17.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.078][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:17.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:17.081][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.082][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.083][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-20 16:02:17.084][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.085][self$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[2025-12-20 16:02:17.086][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.087][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:17.088][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.089][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.090][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.091][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.092][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:17.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:17.094][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.095][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-20 16:02:17.095][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:17.096][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.097][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.098][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.099][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:17.100][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.101][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.102][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:17.103][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.104][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.105][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.106][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:17.107][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:17.108][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.109][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.110][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-20 16:02:17.111][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.112][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:17.113][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.114][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:17.115][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.116][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.117][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.118][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.119][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:17.120][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:17.121][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.122][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-20 16:02:17.123][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:17.124][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.124][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.125][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.126][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:17.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.129][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:17.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.131][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.132][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.132][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:17.134][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:17.135][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.136][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.139][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:17.140][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.153][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.162][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.166][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.170][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.174][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[2025-12-20 16:02:17.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.178][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.182][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.186][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[2025-12-20 16:02:17.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.190][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.195][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.199][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.203][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[2025-12-20 16:02:17.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.207][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.208][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-20 16:02:17.212][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-20 16:02:17.213][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-20 16:02:17.215][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-20 16:02:17.216][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-20 16:02:17.221][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:02:17.222][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:17.223][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:17.225][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-20 16:02:17.226][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:02:17.227][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:02:17.228][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-20 16:02:17.230][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:17.231][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:17.232][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:17.234][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:17.235][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-20 16:02:17.236][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-20 16:02:17.237][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-20 16:02:17.239][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-20 16:02:17.240][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-20 16:02:17.241][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-20 16:02:17.243][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-20 16:02:17.244][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-20 16:02:17.245][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-20 16:02:17.246][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-20 16:02:17.248][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-20 16:02:17.249][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-20 16:02:17.250][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-20 16:02:17.252][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-20 16:02:17.253][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-20 16:02:17.254][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-20 16:02:17.255][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-20 16:02:17.257][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-20 16:02:17.258][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-20 16:02:17.259][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-20 16:02:17.260][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-20 16:02:17.262][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-20 16:02:17.267][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-20 16:02:17.270][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-20 16:02:17.272][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-20 16:02:17.273][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-20 16:02:17.275][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-20 16:02:17.276][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-20 16:02:17.278][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-20 16:02:17.279][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:17.281][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-20 16:02:17.282][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-20 16:02:17.284][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-20 16:02:17.285][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-20 16:02:17.287][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-20 16:02:17.288][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-20 16:02:17.289][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-20 16:02:17.291][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-20 16:02:17.292][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-20 16:02:17.294][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-20 16:02:17.295][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-20 16:02:17.296][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-20 16:02:17.298][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-20 16:02:17.299][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-20 16:02:17.301][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-20 16:02:17.302][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-20 16:02:17.304][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-20 16:02:17.305][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-20 16:02:17.306][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-20 16:02:17.308][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-20 16:02:17.309][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-20 16:02:17.311][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-20 16:02:17.312][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-20 16:02:17.313][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-20 16:02:17.315][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-20 16:02:17.316][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-20 16:02:17.318][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-20 16:02:17.319][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-20 16:02:17.321][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-20 16:02:17.322][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-20 16:02:17.324][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-20 16:02:17.325][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-20 16:02:17.326][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-20 16:02:17.328][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-20 16:02:17.329][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-20 16:02:17.331][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-20 16:02:17.332][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-20 16:02:17.339][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-20 16:02:17.341][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:17.344][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:17.345][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.347][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.348][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.359][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.365][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.371][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.378][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.384][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.403][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.409][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.422][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.428][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.434][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.441][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.447][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.452][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.458][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.464][FUN] Functions in observer BiodbConfig: [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 [2025-12-20 16:02:17.465][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-12-20 16:02:17.473][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-12-20 16:02:17.486][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-12-20 16:02:17.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.491][FUN] Functions in observer BiodbConfig: [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[2025-12-20 16:02:17.493][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:17.501][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-12-20 16:02:17.503][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.504][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.505][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.506][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:17.507][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.508][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-12-20 16:02:17.509][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.511][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:17.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:17.512][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.513][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-12-20 16:02:17.514][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-12-20 16:02:17.515][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-12-20 16:02:17.516][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:17.517][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:17.517][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-12-20 16:02:17.517][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-12-20 16:02:17.518][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:17.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.521][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:17.522][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:17.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:17.523][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:17.524][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-12-20 16:02:17.524][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-12-20 16:02:17.525][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:17.526][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:17.527][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:17.528][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:17.533][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-12-20 16:02:17.534][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:02:17.536][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:02:17.537][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:02:17.539][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:17.563][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-12-20 16:02:17.577][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-12-20 16:02:17.585][biodb::testThat]
biodb.INFO [2025-12-20 16:02:17.586][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-20 16:02:17.587][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:17.588][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:17.591][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-12-20 16:02:17.593][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:02:17.596][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-12-20 16:02:17.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:02:17.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:17.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:17.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:17.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:17.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:02:17.630][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:17.631][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:17.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.633][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:17.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:17.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.649][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:17.650][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:17.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.652][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.676][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:17.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:17.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.680][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.681][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.683][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.684][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.688][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.689][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.691][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.692][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.696][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.699][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.704][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.705][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.707][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.720][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:17.721][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:17.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.723][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.724][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:17.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:17.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.728][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:17.729][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:17.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.731][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:17.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.736][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.737][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.739][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.740][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.744][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.745][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.746][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.748][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.752][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:17.752][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:17.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.754][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.755][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:17.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:17.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.759][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:17.760][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:17.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.762][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:17.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:17.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.767][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:17.768][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:17.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.770][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:17.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:17.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.775][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:17.776][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:17.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.777][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:17.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:17.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.782][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:17.783][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:17.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.785][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:17.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:17.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.790][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:17.791][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:17.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.793][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.794][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:17.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:17.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.797][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:17.798][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:17.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.800][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.801][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:17.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:17.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.805][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-12-20 16:02:17.806][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:17.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.808][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.809][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-12-20 16:02:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:17.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:17.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:17.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:17.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:17.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:17.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.895][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.899][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.902][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:17.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.906][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.910][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.913][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:17.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:17.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:17.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.943][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.946][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:17.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.950][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.957][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:17.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.961][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:17.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:17.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.965][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:17.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:17.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.968][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:17.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:17.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:17.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:17.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:17.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.979][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:17.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:17.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.983][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:17.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:17.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:17.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:17.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.994][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:17.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:17.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:17.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:17.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:17.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:17.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:18.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:18.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:18.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:18.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.020][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.023][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.027][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.053][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.056][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.060][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.064][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.067][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.071][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.075][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.078][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.082][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.085][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-20 16:02:18.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.100][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-12-20 16:02:18.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.124][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.142][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.146][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.153][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:18.179][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-12-20 16:02:18.181][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:18.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:18.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:18.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:18.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:18.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.192][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:18.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:18.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.204][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.239][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.243][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.246][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-12-20 16:02:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.267][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.268][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.270][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.281][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.285][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.289][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.292][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.293][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.295][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.296][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.317][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.318][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.320][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.331][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.335][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.339][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.342][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.343][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.345][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.371][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.372][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.374][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.385][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.389][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.393][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.396][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.397][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.399][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.400][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.417][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.421][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.422][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.424][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:18.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:18.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.438][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:18.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:18.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.442][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.446][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:18.447][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:18.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.448][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.449][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:18.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:18.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:18.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:18.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.463][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:18.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:18.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:18.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:18.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.474][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:18.475][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:18.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.477][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:18.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:18.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.488][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.492][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.495][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.499][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.500][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.501][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.502][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.503][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.524][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.525][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.527][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.538][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.541][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.549][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.550][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.551][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.552][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.562][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.573][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.574][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.576][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.577][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.591][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.595][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.602][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.603][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.605][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.616][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.623][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.627][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.628][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.630][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.630][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:18.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:18.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:18.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:18.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:18.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:18.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.652][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:18.653][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:18.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.654][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:18.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:18.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.677][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.678][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.679][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.690][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.694][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.698][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.705][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.706][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.708][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.709][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.719][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.720][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.722][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.726][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.727][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-12-20 16:02:18.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.729][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.732][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.733][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-12-20 16:02:18.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.735][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.739][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.740][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-12-20 16:02:18.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.742][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.745][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.746][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-12-20 16:02:18.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.748][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.752][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.753][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:18.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.755][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.758][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.759][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:18.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.761][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.765][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.766][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-12-20 16:02:18.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.768][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.771][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:18.772][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:18.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.774][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.778][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:18.779][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:18.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.781][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.784][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:18.785][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:18.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.787][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.791][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.792][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:18.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.794][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.797][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.798][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-12-20 16:02:18.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.800][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.804][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.805][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:18.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.807][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.810][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:18.811][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:18.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.813][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.821][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.822][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:18.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.823][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.827][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.828][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:18.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.830][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.834][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-12-20 16:02:18.835][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-12-20 16:02:18.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.837][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:18.843][biodb::testThat]
biodb.INFO [2025-12-20 16:02:18.844][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-20 16:02:18.845][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:18.845][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:18.858][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-20 16:02:18.860][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:02:18.863][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-20 16:02:18.890][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-20 16:02:18.891][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-20 16:02:18.892][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:19.016][biodb::testThat]
biodb.INFO [2025-12-20 16:02:19.017][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-20 16:02:19.018][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:19.019][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:19.022][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:19.028][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:19.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.030][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:19.031][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-12-20 16:02:19.051][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-20 16:02:19.094][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:02:19.095][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-20 16:02:19.096][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-20 16:02:19.097][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-20 16:02:19.109][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:19.163][biodb::testThat]
biodb.INFO [2025-12-20 16:02:19.164][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-20 16:02:19.165][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:19.165][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:19.172][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-20 16:02:19.173][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:02:19.174][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-20 16:02:19.175][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-20 16:02:19.176][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-20 16:02:19.177][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:19.220][biodb::testThat]
biodb.INFO [2025-12-20 16:02:19.221][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-20 16:02:19.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:19.223][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:19.226][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-12-20 16:02:19.227][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-12-20 16:02:19.228][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-12-20 16:02:19.230][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-12-20 16:02:19.231][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-12-20 16:02:19.232][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:19.270][biodb::testThat]
biodb.INFO [2025-12-20 16:02:19.271][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-20 16:02:19.272][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:19.273][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:19.316][biodb::testThat]
biodb.INFO [2025-12-20 16:02:19.317][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-20 16:02:19.318][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:19.319][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:19.359][biodb::testThat]
biodb.INFO [2025-12-20 16:02:19.360][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:19.361][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:19.362][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-12-20 16:02:19.406][biodb::testThat]
biodb.INFO [2025-12-20 16:02:19.407][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:19.408][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:19.408][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-12-20 16:02:19.460][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:19.461][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:19.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.463][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.464][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:19.465][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:19.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.466][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.467][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:19.468][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:19.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.470][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.471][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:19.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:19.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.474][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.475][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:19.476][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:19.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.477][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.478][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:19.479][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-12-20 16:02:19.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.481][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:19.482][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-20 16:02:19.483][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-12-20 16:02:19.484][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-20 16:02:19.488][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:19.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:19.490][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:19.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:19.492][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:19.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntry(id, drop = TRUE)
 4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
 5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 6.         └─conn$getEntryContent(ids)
 7.           └─self$download()
 8.             └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntry(id, drop = TRUE)
 4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
 5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 6.         └─conn$getEntryContent(ids)
 7.           └─self$download()
 8.             └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─private$bdb$getFactory()$getEntry(...)
 6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 7.           └─conn$getEntryContent(ids)
 8.             └─self$download()
 9.               └─private$doExtractDownload()
── Error ('test_long_100_generic.R:42:1'): We can get a URL pointing to the entry page. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): We can get a URL pointing to the entry image. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): The entry page URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbHmdb (local) FUN(X[[i]], ...)

[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)