Back to Long Tests report for BioC 3.22

This page was generated on 2026-01-31 23:55 -0500 (Sat, 31 Jan 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4888
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4678
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-01-31 16:01:16 -0500 (Sat, 31 Jan 2026)
EndedAt: 2026-01-31 16:02:45 -0500 (Sat, 31 Jan 2026)
EllapsedTime: 89.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2026-01-31 16:02:39.928][biodb::testContext]
biodb.INFO [2026-01-31 16:02:39.931][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:39.933][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-01-31 16:02:39.934][biodb::testContext] ********************************************************************************
biodb.INFO [2026-01-31 16:02:39.935][biodb::testContext]
biodb.INFO [2026-01-31 16:02:39.942][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:39.944][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:39.952][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:39.953][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-01-31 16:02:39.955][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-01-31 16:02:39.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:39.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:39.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:39.959][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-01-31 16:02:39.984][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-01-31 16:02:39.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:39.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:39.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:39.989][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-01-31 16:02:39.990][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-01-31 16:02:39.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:39.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:39.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:39.995][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-01-31 16:02:39.996][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-01-31 16:02:39.997][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-01-31 16:02:39.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.002][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-01-31 16:02:40.003][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-01-31 16:02:40.005][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-01-31 16:02:40.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.009][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-01-31 16:02:40.011][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-01-31 16:02:40.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.015][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-01-31 16:02:40.017][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-01-31 16:02:40.018][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-01-31 16:02:40.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.023][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-01-31 16:02:40.024][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-01-31 16:02:40.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.029][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-01-31 16:02:40.030][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-01-31 16:02:40.031][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-01-31 16:02:40.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.036][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:40.037][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-01-31 16:02:40.039][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-01-31 16:02:40.040][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-01-31 16:02:40.041][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-01-31 16:02:40.043][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-01-31 16:02:40.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.047][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-01-31 16:02:40.049][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-01-31 16:02:40.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.053][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-01-31 16:02:40.055][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-01-31 16:02:40.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.060][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-01-31 16:02:40.061][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-01-31 16:02:40.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.066][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-01-31 16:02:40.067][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-01-31 16:02:40.069][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-01-31 16:02:40.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.073][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-01-31 16:02:40.075][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-01-31 16:02:40.085][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-01-31 16:02:40.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.090][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-01-31 16:02:40.092][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-01-31 16:02:40.093][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-01-31 16:02:40.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.100][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-01-31 16:02:40.144][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.172][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-01-31 16:02:40.173][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.174][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:40.175][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.177][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.178][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.179][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.180][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:40.182][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:40.183][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.184][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-01-31 16:02:40.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:40.186][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.188][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.189][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:40.189][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:40.189][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:40.189][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:40.189][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:40.190][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:40.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.194][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:40.195][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.196][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.197][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.199][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.200][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:40.201][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:40.202][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.203][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.205][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-01-31 16:02:40.207][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.208][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:40.210][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.211][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:40.212][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.213][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.214][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.216][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.217][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:40.218][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:40.219][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.221][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-01-31 16:02:40.222][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:40.223][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.224][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.226][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:40.226][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-01-31 16:02:40.226][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-01-31 16:02:40.226][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-01-31 16:02:40.226][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-01-31 16:02:40.227][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:40.228][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.229][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.231][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:40.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.234][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.235][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.236][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:40.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:40.239][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.240][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.242][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-01-31 16:02:40.244][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.245][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-01-31 16:02:40.246][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.248][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:40.249][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.250][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.251][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.253][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.254][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-01-31 16:02:40.255][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:40.256][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.258][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-01-31 16:02:40.259][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:40.260][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.261][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.263][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.264][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:40.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.267][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:40.268][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.271][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.272][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.273][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:40.274][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:40.276][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.277][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.278][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-01-31 16:02:40.280][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.282][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-01-31 16:02:40.283][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.284][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:40.286][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.287][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.288][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.289][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.291][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-01-31 16:02:40.292][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:40.293][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.294][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-01-31 16:02:40.296][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:40.297][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.298][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.299][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.301][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-01-31 16:02:40.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.304][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:40.305][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.308][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.309][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.310][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:40.311][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:40.312][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.314][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.318][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:40.319][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.348][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[2026-01-31 16:02:40.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.365][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[2026-01-31 16:02:40.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.371][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[2026-01-31 16:02:40.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.416][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-01-31 16:02:40.421][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-01-31 16:02:40.423][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-01-31 16:02:40.425][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-01-31 16:02:40.426][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-01-31 16:02:40.428][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:40.430][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:40.431][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:40.433][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-01-31 16:02:40.435][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:40.436][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:40.438][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-01-31 16:02:40.440][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-01-31 16:02:40.441][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-01-31 16:02:40.443][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-01-31 16:02:40.445][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:40.446][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-01-31 16:02:40.448][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-01-31 16:02:40.450][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-01-31 16:02:40.451][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-01-31 16:02:40.453][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-01-31 16:02:40.455][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-01-31 16:02:40.457][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-01-31 16:02:40.458][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-01-31 16:02:40.460][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-01-31 16:02:40.462][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-01-31 16:02:40.464][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-01-31 16:02:40.465][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-01-31 16:02:40.467][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-01-31 16:02:40.469][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-01-31 16:02:40.471][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-01-31 16:02:40.472][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-01-31 16:02:40.474][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-01-31 16:02:40.476][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-01-31 16:02:40.477][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-01-31 16:02:40.479][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-01-31 16:02:40.481][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-01-31 16:02:40.483][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-01-31 16:02:40.484][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-01-31 16:02:40.486][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-01-31 16:02:40.488][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-01-31 16:02:40.489][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-01-31 16:02:40.491][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-01-31 16:02:40.493][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-01-31 16:02:40.494][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-01-31 16:02:40.496][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-01-31 16:02:40.498][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-01-31 16:02:40.500][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-01-31 16:02:40.501][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-01-31 16:02:40.503][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-01-31 16:02:40.505][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-01-31 16:02:40.506][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-01-31 16:02:40.508][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-01-31 16:02:40.510][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-01-31 16:02:40.511][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-01-31 16:02:40.513][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-01-31 16:02:40.515][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-01-31 16:02:40.517][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-01-31 16:02:40.518][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-01-31 16:02:40.520][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-01-31 16:02:40.522][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-01-31 16:02:40.524][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-01-31 16:02:40.526][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-01-31 16:02:40.527][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-01-31 16:02:40.529][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-01-31 16:02:40.531][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-01-31 16:02:40.533][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-01-31 16:02:40.535][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-01-31 16:02:40.536][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-01-31 16:02:40.538][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-01-31 16:02:40.540][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-01-31 16:02:40.542][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-01-31 16:02:40.544][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-01-31 16:02:40.545][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-01-31 16:02:40.547][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-01-31 16:02:40.549][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-01-31 16:02:40.551][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-01-31 16:02:40.553][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-01-31 16:02:40.555][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-01-31 16:02:40.557][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-01-31 16:02:40.558][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-01-31 16:02:40.560][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-01-31 16:02:40.562][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-01-31 16:02:40.570][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-01-31 16:02:40.572][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-01-31 16:02:40.576][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-01-31 16:02:40.577][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.579][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2026-01-31 16:02:40.714][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-01-31 16:02:40.724][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-01-31 16:02:40.742][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-01-31 16:02:40.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-01-31 16:02:40.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-01-31 16:02:40.752][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-01-31 16:02:40.765][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-01-31 16:02:40.767][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.769][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.770][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.771][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-01-31 16:02:40.772][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.773][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-01-31 16:02:40.775][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.776][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.777][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-01-31 16:02:40.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-01-31 16:02:40.780][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.781][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-01-31 16:02:40.782][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-01-31 16:02:40.783][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-01-31 16:02:40.785][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-01-31 16:02:40.786][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-01-31 16:02:40.786][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-01-31 16:02:40.786][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-01-31 16:02:40.787][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-01-31 16:02:40.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.791][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-01-31 16:02:40.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-01-31 16:02:40.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-01-31 16:02:40.794][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-01-31 16:02:40.795][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-01-31 16:02:40.795][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-01-31 16:02:40.797][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-01-31 16:02:40.798][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-01-31 16:02:40.799][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-01-31 16:02:40.800][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-01-31 16:02:40.808][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-01-31 16:02:40.810][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-01-31 16:02:40.812][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-01-31 16:02:40.814][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-01-31 16:02:40.815][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-01-31 16:02:40.838][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-01-31 16:02:40.859][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-01-31 16:02:40.870][biodb::testThat]
biodb.INFO [2026-01-31 16:02:40.872][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-01-31 16:02:40.873][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:40.874][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:40.879][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-01-31 16:02:40.881][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-01-31 16:02:40.885][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-01-31 16:02:40.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-01-31 16:02:40.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:40.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:40.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:40.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:40.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:40.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-01-31 16:02:40.929][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:40.930][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:40.932][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:40.933][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:40.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:40.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:40.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:40.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:40.966][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:40.967][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:40.969][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:40.970][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.006][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.012][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.013][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.014][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.015][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.017][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.022][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.024][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.025][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.026][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.028][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.033][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.034][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.035][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.037][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.043][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.045][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.046][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.047][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.054][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.055][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.056][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.058][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.059][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.064][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.066][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.067][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.068][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.070][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.075][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.076][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.078][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.079][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.086][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.087][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.088][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.089][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.091][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.096][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:41.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:41.099][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.100][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:41.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:41.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.107][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:41.108][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:41.109][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.110][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:41.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:41.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.117][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.118][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.120][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.121][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.128][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.129][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.130][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.131][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.138][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.139][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.140][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.142][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.148][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:41.150][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:41.151][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.152][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.154][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.163][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:41.164][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:41.166][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.167][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.168][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.173][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-01-31 16:02:41.175][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:41.176][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.177][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.179][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-01-31 16:02:41.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:41.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.244][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.250][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.255][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:41.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.260][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.265][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.270][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:41.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.317][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:41.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:41.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:41.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:41.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.342][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:41.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:41.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:41.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:41.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.352][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:41.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:41.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.357][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:41.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:41.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.362][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:41.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:41.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:41.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:41.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.376][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:41.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:41.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.381][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:41.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:41.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:41.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:41.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:41.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:41.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:41.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:41.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.415][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.420][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.425][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.435][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:41.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.460][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.465][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.470][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.475][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.480][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.485][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.490][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:41.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:41.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.495][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:41.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:41.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.499][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:41.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:41.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.504][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-31 16:02:41.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.524][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-01-31 16:02:41.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:41.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.610][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.615][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.625][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:41.660][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-01-31 16:02:41.663][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:41.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:41.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.668][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-01-31 16:02:41.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-01-31 16:02:41.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:41.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-01-31 16:02:41.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.678][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:41.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-01-31 16:02:41.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.696][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.739][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.744][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.749][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-01-31 16:02:41.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.779][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.780][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.781][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.782][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:41.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:41.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.800][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.805][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.810][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.815][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.817][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.818][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.819][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.820][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:41.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.857][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.858][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.859][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.860][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:41.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.877][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.883][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.888][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.893][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.895][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.896][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.897][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.898][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:41.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.930][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.931][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.933][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.934][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:41.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.951][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.956][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.961][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.967][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.968][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.969][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.970][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.972][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:41.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:41.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:41.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:41.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:41.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:42.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.003][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:42.004][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:42.005][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.006][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:42.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:42.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.024][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:42.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:42.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.029][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:42.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:42.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.034][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:42.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:42.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.039][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:42.041][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:42.042][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.043][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.044][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:42.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:42.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.066][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:42.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:42.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.073][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:42.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:42.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:42.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:42.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.083][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:42.085][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:42.086][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.087][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:42.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:42.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.105][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.111][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.116][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.122][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.123][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.125][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.126][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.127][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.161][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.162][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.163][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.164][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.182][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.192][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.198][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.200][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.201][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.202][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.203][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.221][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.227][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.232][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.238][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.240][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.241][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.242][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.261][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.267][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.277][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.279][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.280][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.281][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.283][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:42.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:42.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.309][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:42.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:42.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.314][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:42.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:42.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.319][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:42.320][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:42.322][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.323][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.324][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:42.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:42.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:42.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:42.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:42.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:42.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:42.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:42.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.355][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:42.356][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:42.358][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.359][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:42.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:42.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.386][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.391][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.392][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.393][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.394][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.411][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.416][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.421][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.426][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.427][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.428][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.430][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.431][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.446][ef$get] Asked field names are: accession.
biodb.TRACE[2026-01-31 16:02:42.448][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-01-31 16:02:42.449][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.450][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.456][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.458][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-01-31 16:02:42.459][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.460][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.467][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.468][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-01-31 16:02:42.469][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.470][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.477][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-01-31 16:02:42.478][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-01-31 16:02:42.479][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.481][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.487][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:42.488][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-01-31 16:02:42.489][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.490][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.497][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.498][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-01-31 16:02:42.499][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.501][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.507][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.509][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-01-31 16:02:42.510][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.511][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.517][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.519][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-01-31 16:02:42.520][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.521][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.532][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:42.533][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:42.535][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.536][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.542][ef$get] Asked field names are: formula.
biodb.TRACE[2026-01-31 16:02:42.543][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-01-31 16:02:42.544][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.546][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.552][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-01-31 16:02:42.553][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-01-31 16:02:42.555][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.556][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.562][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.563][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-01-31 16:02:42.565][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.566][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.572][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:42.574][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-01-31 16:02:42.575][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.576][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.585][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.587][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-01-31 16:02:42.590][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.592][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.599][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:42.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:42.603][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.604][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.611][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:42.612][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-01-31 16:02:42.613][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.615][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.624][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:42.626][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:42.628][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.629][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:42.636][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-01-31 16:02:42.638][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-01-31 16:02:42.639][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.640][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:42.652][biodb::testThat]
biodb.INFO [2026-01-31 16:02:42.653][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-01-31 16:02:42.655][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:42.656][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:42.678][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-31 16:02:42.684][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:42.688][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:42.730][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-31 16:02:42.732][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-31 16:02:42.733][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:42.916][biodb::testThat]
biodb.INFO [2026-01-31 16:02:42.917][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-01-31 16:02:42.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:42.920][biodb::testThat]
biodb.TRACE[2026-01-31 16:02:42.924][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:42.926][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:42.927][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:42.928][ef$get] fields variable is a list.
biodb.DEBUG[2026-01-31 16:02:42.930][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-01-31 16:02:42.961][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-31 16:02:43.030][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:43.032][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:43.034][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-31 16:02:43.036][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-31 16:02:43.053][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:43.125][biodb::testThat]
biodb.INFO [2026-01-31 16:02:43.126][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-01-31 16:02:43.127][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:43.128][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:43.138][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-31 16:02:43.140][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:43.141][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:43.143][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-31 16:02:43.145][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-31 16:02:43.146][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:43.211][biodb::testThat]
biodb.INFO [2026-01-31 16:02:43.213][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-01-31 16:02:43.214][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:43.215][biodb::testThat]
biodb.DEBUG[2026-01-31 16:02:43.220][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-01-31 16:02:43.222][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-01-31 16:02:43.224][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-01-31 16:02:43.225][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-01-31 16:02:43.227][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-01-31 16:02:43.228][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:43.306][biodb::testThat]
biodb.INFO [2026-01-31 16:02:43.308][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-01-31 16:02:43.310][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:43.312][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:43.382][biodb::testThat]
biodb.INFO [2026-01-31 16:02:43.383][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-01-31 16:02:43.384][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:43.386][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:43.446][biodb::testThat]
biodb.INFO [2026-01-31 16:02:43.448][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:43.449][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:43.450][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-01-31 16:02:43.515][biodb::testThat]
biodb.INFO [2026-01-31 16:02:43.516][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-01-31 16:02:43.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-01-31 16:02:43.518][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-01-31 16:02:43.602][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:43.603][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:43.605][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:43.606][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:43.607][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:43.608][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:43.610][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:43.611][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:43.612][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:43.614][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:43.615][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:43.616][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:43.618][ef$get] Asked field names are: name.
biodb.TRACE[2026-01-31 16:02:43.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-01-31 16:02:43.620][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:43.622][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:43.623][ef$get] Asked field names are: description.
biodb.TRACE[2026-01-31 16:02:43.624][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-01-31 16:02:43.625][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:43.627][ef$get] fields variable is a list.
biodb.TRACE[2026-01-31 16:02:43.628][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:43.629][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-01-31 16:02:43.631][ef$get] 1 fields were returned.
biodb.TRACE[2026-01-31 16:02:43.632][ef$get] fields variable is a list.
biodb.INFO [2026-01-31 16:02:43.633][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-01-31 16:02:43.635][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-01-31 16:02:43.636][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-01-31 16:02:43.637][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-01-31 16:02:43.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-01-31 16:02:43.639][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-01-31 16:02:43.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-01-31 16:02:43.641][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-01-31 16:02:43.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
   5.       └─base::vapply(id, fct, FUN.VALUE = "")
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.16.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)