Back to Long Tests report for BioC 3.22

This page was generated on 2026-03-28 23:55 -0400 (Sat, 28 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4893
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4687
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-03-28 09:55 -0400 (Sat, 28 Mar 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-03-28 16:01:22 -0400 (Sat, 28 Mar 2026)
EndedAt: 2026-03-28 16:02:52 -0400 (Sat, 28 Mar 2026)
EllapsedTime: 89.9 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 [2026-03-28 16:02:46.769][biodb::testContext]
biodb.INFO [2026-03-28 16:02:46.773][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:46.774][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-03-28 16:02:46.775][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:46.776][biodb::testContext]
biodb.INFO [2026-03-28 16:02:46.783][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:46.785][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:46.793][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:46.795][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:02:46.796][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:02:46.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.801][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:02:46.825][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:02:46.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.830][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:02:46.831][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:02:46.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.836][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:02:46.837][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:02:46.839][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:02:46.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.844][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:02:46.845][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:02:46.846][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:02:46.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.851][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:02:46.852][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:02:46.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.857][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:02:46.858][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:02:46.859][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:02:46.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.864][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:02:46.865][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:02:46.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.870][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:02:46.871][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:02:46.872][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:02:46.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.877][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:46.878][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:02:46.879][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:02:46.881][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:02:46.882][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:02:46.883][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:02:46.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.888][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:02:46.889][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:02:46.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.894][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:02:46.895][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:02:46.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.899][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:02:46.901][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:02:46.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.905][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:02:46.907][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:02:46.908][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:02:46.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.912][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:46.914][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:02:46.924][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:02:46.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.929][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:02:46.931][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:02:46.932][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:02:46.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:46.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:46.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:46.940][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:02:46.984][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.012][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-28 16:02:47.014][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.015][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:47.016][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.018][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.021][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:47.023][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:47.024][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.025][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:02:47.026][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:47.028][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.029][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.030][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:47.030][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:47.030][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:47.030][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:47.030][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:47.032][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:47.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:47.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.039][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.040][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.041][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:47.042][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:47.044][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.045][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.046][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:02:47.049][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.050][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:47.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:47.054][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.055][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.056][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.058][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.059][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:47.060][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:47.061][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.063][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:02:47.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:47.065][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.067][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.068][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:47.068][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:47.068][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:47.068][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:47.068][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:47.069][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:47.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.073][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:47.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.078][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:47.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:47.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.083][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.084][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:02:47.087][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.088][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-28 16:02:47.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:47.092][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.093][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.095][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.097][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:47.098][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:47.100][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.102][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:02:47.104][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:47.106][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.107][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.109][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.110][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:47.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:47.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.120][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.121][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:47.122][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:47.124][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.126][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.127][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:02:47.130][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.131][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:47.132][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:47.135][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.136][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.137][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.138][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.140][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:47.141][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:47.142][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.144][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:02:47.145][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:47.146][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.147][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.149][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.150][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:47.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.154][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:47.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.158][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.159][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.161][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:47.162][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:47.163][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.164][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.168][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:47.169][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.266][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:02:47.270][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:02:47.272][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:02:47.278][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:02:47.280][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:02:47.282][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:02:47.283][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:47.285][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:47.287][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:02:47.289][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:02:47.290][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:02:47.292][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:02:47.294][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:47.295][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:47.297][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:47.299][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:47.300][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:02:47.302][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:02:47.304][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:02:47.306][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:02:47.307][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:02:47.309][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:02:47.311][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:02:47.313][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:02:47.314][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:02:47.316][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:02:47.318][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:02:47.320][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:02:47.321][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:02:47.323][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:02:47.325][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:02:47.327][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:02:47.328][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:02:47.330][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:02:47.332][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:02:47.334][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:02:47.336][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:02:47.337][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:02:47.339][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:02:47.341][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:02:47.343][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:02:47.345][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:02:47.346][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:02:47.348][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:02:47.350][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:02:47.351][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:47.353][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:02:47.355][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:02:47.357][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:02:47.358][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:02:47.360][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:02:47.362][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:02:47.363][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:02:47.365][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:02:47.367][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:02:47.368][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:02:47.370][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:02:47.372][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:02:47.374][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:02:47.375][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:02:47.377][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:02:47.379][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:02:47.381][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:02:47.382][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:02:47.384][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:02:47.386][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:02:47.387][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:02:47.389][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:02:47.391][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:02:47.392][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:02:47.394][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:02:47.396][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:02:47.398][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:02:47.400][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:02:47.401][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:02:47.403][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:02:47.405][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:02:47.407][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:02:47.409][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:02:47.411][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:02:47.412][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:02:47.414][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:02:47.416][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:02:47.423][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:02:47.426][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:47.429][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:47.430][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.433][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2026-03-28 16:02:47.574][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-03-28 16:02:47.585][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-03-28 16:02:47.603][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-03-28 16:02:47.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:47.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:47.614][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:47.627][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-03-28 16:02:47.629][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.631][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.632][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.633][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:47.635][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.636][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-03-28 16:02:47.637][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.640][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-03-28 16:02:47.641][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:47.642][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.644][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-03-28 16:02:47.645][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-03-28 16:02:47.646][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-03-28 16:02:47.648][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:47.650][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:47.650][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-03-28 16:02:47.650][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-03-28 16:02:47.651][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:47.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.655][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:47.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:47.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:47.659][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:47.660][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-03-28 16:02:47.660][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-03-28 16:02:47.661][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:47.662][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:47.664][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:47.665][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:47.673][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-03-28 16:02:47.675][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:02:47.676][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:02:47.678][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:02:47.680][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:47.703][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-03-28 16:02:47.719][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-03-28 16:02:47.729][biodb::testThat]
biodb.INFO [2026-03-28 16:02:47.731][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-28 16:02:47.732][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:47.733][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:47.738][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-03-28 16:02:47.740][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:47.744][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-03-28 16:02:47.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:47.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:47.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:47.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:47.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:47.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:47.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:47.787][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:47.788][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:47.789][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.791][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:47.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:47.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.824][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:47.825][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:47.826][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.827][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.862][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:47.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:47.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.868][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:47.869][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:47.870][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.872][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.873][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:47.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:47.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.878][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:47.880][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:47.881][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.882][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.884][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:47.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:47.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:47.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:47.892][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.893][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:47.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:47.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.900][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:47.901][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:47.902][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.903][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:47.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:47.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.910][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:47.911][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:47.913][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.914][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.915][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:47.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:47.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.921][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:47.922][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:47.923][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.924][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.926][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:47.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:47.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.931][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:47.933][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:47.934][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.935][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.937][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:47.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:47.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.942][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:47.943][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:47.945][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.946][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.947][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:47.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:47.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.953][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:47.954][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:47.955][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.956][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:47.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:47.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.963][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:47.964][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:47.966][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.967][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:47.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:47.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.973][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:47.975][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:47.976][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.977][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.979][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:47.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:47.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.984][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:47.985][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:47.987][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.988][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:47.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:47.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:47.995][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:47.996][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:47.997][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:47.998][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.005][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.007][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.008][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.009][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.010][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.016][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:48.017][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:48.018][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.019][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.021][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:48.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:48.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.026][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-03-28 16:02:48.028][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:48.029][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.030][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.032][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-03-28 16:02:48.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:48.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.101][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:48.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:48.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.106][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:48.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:48.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.111][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:48.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:48.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.116][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:48.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:48.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.122][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:48.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:48.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.127][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:48.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:48.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:48.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:48.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:48.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:48.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.173][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:48.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:48.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.178][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:48.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:48.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.183][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:48.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:48.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.188][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:48.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:48.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.194][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:48.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:48.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.199][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:48.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:48.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.204][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:48.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:48.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.209][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.214][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.219][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.224][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:48.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:48.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.229][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:48.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:48.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:48.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:48.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:48.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:48.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:48.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:48.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:48.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:48.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.274][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.279][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.284][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:48.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:48.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:48.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:48.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:48.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:48.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.319][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.325][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.335][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.340][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.345][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.350][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:48.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:48.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.355][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:48.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:48.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.360][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:48.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:48.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.365][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-03-28 16:02:48.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.385][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-03-28 16:02:48.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:48.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.419][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.430][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.440][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.445][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.456][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:48.529][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-03-28 16:02:48.532][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:48.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:48.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:48.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:48.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.543][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:48.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:48.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.548][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:48.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:48.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.643][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.688][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.693][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.698][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-03-28 16:02:48.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.731][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.732][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.734][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.735][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:48.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:48.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.752][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.758][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.763][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.768][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.770][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.771][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.772][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.773][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:48.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.805][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.806][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.807][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.809][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:48.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.831][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.837][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.842][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.847][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.848][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.850][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.851][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.852][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:48.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.883][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.885][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.886][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.887][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:48.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.904][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.910][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.915][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.920][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.922][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.923][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.924][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.926][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:48.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.957][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.959][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.960][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.961][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:48.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:48.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.978][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.983][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.988][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.994][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:48.995][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:48.996][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:48.997][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:48.999][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:49.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:49.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.014][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:49.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:49.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.020][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:49.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:49.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.025][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:49.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:49.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.030][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:49.031][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:49.032][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.033][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.035][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:49.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:49.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.054][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.060][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.065][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.070][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.071][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.072][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.073][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.075][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.107][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.108][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.109][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.110][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.128][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.134][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.139][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.144][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.146][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.147][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.148][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.150][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.166][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.177][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.182][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.183][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.185][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.186][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.203][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.210][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.216][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.222][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.224][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.225][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.226][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.228][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.245][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:49.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:49.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.252][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:49.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:49.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.257][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:49.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:49.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.262][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:49.264][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:49.265][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.266][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.267][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:49.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:49.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:49.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:49.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:49.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:49.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:49.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:49.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.320][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:49.322][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:49.324][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.325][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.327][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:49.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:49.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.369][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.372][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.374][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.376][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.399][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.404][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.409][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.415][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.416][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.417][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.418][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.420][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.436][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:49.438][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:49.439][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.440][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.447][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.448][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-03-28 16:02:49.450][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.451][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.459][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.462][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:49.464][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.466][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.473][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-03-28 16:02:49.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-03-28 16:02:49.475][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.477][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.483][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:49.485][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-03-28 16:02:49.486][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.487][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.494][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.496][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-03-28 16:02:49.497][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.498][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.505][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.506][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-03-28 16:02:49.508][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.509][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.516][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.518][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-03-28 16:02:49.519][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.521][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.527][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:49.529][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:49.530][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.531][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.538][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:49.540][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:49.541][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.542][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.549][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:49.550][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:49.551][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.553][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.559][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.561][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:49.562][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.564][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.575][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:49.577][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-03-28 16:02:49.578][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.579][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.586][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.588][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-03-28 16:02:49.589][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.590][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.598][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:49.599][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:49.601][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.602][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.609][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:49.610][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-03-28 16:02:49.611][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.613][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.619][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:49.621][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:49.622][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.623][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:49.630][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-03-28 16:02:49.631][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-03-28 16:02:49.632][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.634][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:02:49.645][biodb::testThat]
biodb.INFO [2026-03-28 16:02:49.647][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-28 16:02:49.648][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:49.650][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:49.673][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-28 16:02:49.678][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-28 16:02:49.681][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-28 16:02:49.721][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-28 16:02:49.723][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-28 16:02:49.724][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-28 16:02:49.904][biodb::testThat]
biodb.INFO [2026-03-28 16:02:49.905][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-28 16:02:49.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:49.907][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:49.911][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:49.913][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:49.914][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:49.915][ef$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:49.917][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-03-28 16:02:49.947][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-28 16:02:50.048][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-28 16:02:50.052][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-28 16:02:50.055][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-28 16:02:50.058][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-28 16:02:50.088][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-28 16:02:50.166][biodb::testThat]
biodb.INFO [2026-03-28 16:02:50.167][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-28 16:02:50.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:50.171][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:50.184][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-28 16:02:50.186][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-28 16:02:50.188][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-28 16:02:50.189][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-28 16:02:50.191][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-28 16:02:50.192][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-28 16:02:50.276][biodb::testThat]
biodb.INFO [2026-03-28 16:02:50.278][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-28 16:02:50.279][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:50.281][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:50.286][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-03-28 16:02:50.288][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-28 16:02:50.290][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-03-28 16:02:50.294][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-03-28 16:02:50.297][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-03-28 16:02:50.299][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-28 16:02:50.358][biodb::testThat]
biodb.INFO [2026-03-28 16:02:50.359][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-28 16:02:50.360][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:50.361][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-28 16:02:50.419][biodb::testThat]
biodb.INFO [2026-03-28 16:02:50.420][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-28 16:02:50.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:50.422][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-28 16:02:50.483][biodb::testThat]
biodb.INFO [2026-03-28 16:02:50.485][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:50.486][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:50.487][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-03-28 16:02:50.545][biodb::testThat]
biodb.INFO [2026-03-28 16:02:50.546][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:50.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:50.548][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-03-28 16:02:50.627][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:50.628][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:50.629][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:50.631][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:50.632][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:50.633][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:50.634][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:50.635][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:50.637][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:50.638][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:50.639][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:50.640][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:50.642][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:50.643][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:50.644][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:50.645][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:50.646][ef$get] Asked field names are: description.
biodb.TRACE[2026-03-28 16:02:50.648][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-03-28 16:02:50.649][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:50.650][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:50.651][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:50.653][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-03-28 16:02:50.654][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:50.655][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:02:50.656][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:02:50.658][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-03-28 16:02:50.659][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:02:50.660][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:50.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:50.662][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:50.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:50.664][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:50.665][FUN] Functions in observer 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)