Back to Long Tests report for BioC 3.22

This page was generated on 2026-02-21 23:55 -0500 (Sat, 21 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4890
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4680
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: 2026-02-21 09:55 -0500 (Sat, 21 Feb 2026)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on merida1

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-02-21 16:01:21 -0500 (Sat, 21 Feb 2026)
EndedAt: 2026-02-21 16:02:58 -0500 (Sat, 21 Feb 2026)
EllapsedTime: 96.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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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 [2026-02-21 16:02:54.135][biodb::testContext]
biodb.INFO [2026-02-21 16:02:54.139][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:54.140][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-21 16:02:54.142][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:54.143][biodb::testContext]
biodb.INFO [2026-02-21 16:02:54.149][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:54.151][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:54.159][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:54.160][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:02:54.162][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:02:54.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.171][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:02:54.204][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:02:54.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.209][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:02:54.211][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:02:54.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.218][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:02:54.219][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:02:54.220][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:02:54.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.227][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:02:54.228][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:02:54.230][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:02:54.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.234][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:02:54.236][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:02:54.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.239][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.240][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:02:54.242][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:02:54.243][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:02:54.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.248][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:02:54.249][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:02:54.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.252][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.253][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:02:54.255][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:02:54.256][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:02:54.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.261][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:54.262][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:02:54.263][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:02:54.264][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:02:54.266][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:02:54.267][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:02:54.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.270][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.272][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:02:54.273][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:02:54.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.278][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:02:54.279][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:02:54.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.282][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.283][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:02:54.285][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:02:54.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.289][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:02:54.291][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:02:54.292][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:02:54.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.295][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.296][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:54.298][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:02:54.308][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:02:54.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.313][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:02:54.315][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:02:54.316][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:02:54.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.319][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.323][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:02:54.368][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.396][self$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[2026-02-21 16:02:54.398][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.399][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:54.400][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.402][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.403][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.404][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.405][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:54.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:54.408][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.409][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:02:54.410][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:54.412][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.413][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.414][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:54.414][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:54.414][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:54.414][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:54.414][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:54.416][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:54.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:54.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:54.419][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:54.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:54.422][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:54.423][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.424][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.425][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:54.426][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:54.428][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.429][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.430][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:02:54.433][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.434][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:54.435][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.437][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:54.438][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.439][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.440][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.442][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.443][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:54.444][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:54.445][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.447][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:02:54.448][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:54.449][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.450][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.452][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:54.452][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:54.452][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:54.452][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:54.452][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:54.453][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:54.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:54.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:54.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:54.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:54.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:54.460][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.462][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.463][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:54.464][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:54.465][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.467][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.468][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:02:54.471][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.472][self$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[2026-02-21 16:02:54.474][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.475][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:54.476][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.478][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.479][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.480][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.482][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:54.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:54.484][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.486][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:02:54.487][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:54.488][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.489][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.491][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.493][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:54.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:54.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:54.498][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:54.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:54.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:54.502][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.503][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.504][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:54.505][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:54.507][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.508][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.509][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:02:54.512][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.513][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:54.514][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.516][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:54.517][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.518][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.519][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.521][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.522][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:54.523][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:54.524][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.526][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:02:54.527][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:54.528][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.529][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.530][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.532][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:54.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:54.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:54.535][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:54.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:54.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:54.539][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.540][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:54.542][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:54.543][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.545][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:54.549][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:54.550][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.551][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.557][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[2026-02-21 16:02:54.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.562][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.568][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.574][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.579][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.585][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.590][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.596][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.602][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.608][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.614][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.625][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.630][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.636][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.646][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.647][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:02:54.652][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:02:54.654][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:02:54.656][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:02:54.657][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:02:54.659][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:54.661][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:54.663][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:54.664][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:02:54.666][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:54.668][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:54.670][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:02:54.671][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:54.673][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:54.675][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:54.676][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:54.678][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:02:54.679][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:02:54.681][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:02:54.683][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:02:54.685][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:02:54.686][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:02:54.688][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:02:54.690][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:02:54.691][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:02:54.693][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:02:54.695][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:02:54.696][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:02:54.698][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:02:54.700][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:02:54.701][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:02:54.703][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:02:54.705][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:02:54.706][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:02:54.708][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:02:54.710][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:02:54.711][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:02:54.713][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:02:54.715][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:02:54.716][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:02:54.718][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:02:54.719][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:02:54.721][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:02:54.723][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:02:54.724][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:02:54.726][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:54.728][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:02:54.729][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:02:54.731][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:02:54.733][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:02:54.734][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:02:54.736][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:02:54.738][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:02:54.739][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:02:54.741][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:02:54.743][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:02:54.744][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:02:54.746][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:02:54.748][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:02:54.749][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:02:54.751][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:02:54.753][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:02:54.754][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:02:54.756][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:02:54.758][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:02:54.759][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:02:54.761][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:02:54.762][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:02:54.764][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:02:54.766][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:02:54.767][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:02:54.769][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:02:54.771][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:02:54.772][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:02:54.774][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:02:54.776][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:02:54.777][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:02:54.779][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:02:54.781][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:02:54.782][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:02:54.784][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:02:54.786][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:02:54.787][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:02:54.794][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:02:54.796][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:54.800][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:54.801][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.803][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.804][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.817][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.824][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.832][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.839][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.847][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.854][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.870][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.885][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.905][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:54.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.927][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.935][FUN] Functions in observer BiodbConfig: [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 [2026-02-21 16:02:54.936][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-02-21 16:02:54.946][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2026-02-21 16:02:54.964][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-02-21 16:02:54.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:54.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:54.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:54.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:54.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:54.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:54.972][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:54.974][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:54.987][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-02-21 16:02:54.989][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.990][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.991][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.993][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:54.994][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:54.995][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-02-21 16:02:54.996][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:54.998][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:54.999][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:55.000][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:55.001][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:55.002][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-02-21 16:02:55.004][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-02-21 16:02:55.005][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-02-21 16:02:55.006][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:55.008][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:55.008][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-02-21 16:02:55.008][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-02-21 16:02:55.009][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:55.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:55.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:55.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:55.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:55.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:55.016][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:55.017][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-02-21 16:02:55.017][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-02-21 16:02:55.019][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:55.020][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:55.021][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:55.022][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:55.030][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-02-21 16:02:55.032][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:55.033][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:55.035][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:55.037][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:55.058][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-02-21 16:02:55.074][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-02-21 16:02:55.084][biodb::testThat]
biodb.INFO [2026-02-21 16:02:55.085][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-21 16:02:55.086][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:55.087][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:55.092][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[2026-02-21 16:02:55.094][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:55.098][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-02-21 16:02:55.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:55.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:55.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:55.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:55.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:55.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:55.128][FUN] Functions in observer BiodbConfig: [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[2026-02-21 16:02:55.140][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.142][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.143][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.144][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.176][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.178][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.179][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.180][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.215][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.220][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.221][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.223][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.224][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.225][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.230][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.232][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.233][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.234][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.235][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.240][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.242][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.243][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.244][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.251][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.252][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.253][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.254][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.261][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.262][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.264][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.265][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.266][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.271][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.273][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.274][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.275][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.276][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.281][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.283][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.284][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.285][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.286][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.291][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.293][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.294][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.295][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.296][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.301][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:55.303][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:55.304][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.305][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:55.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:55.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.311][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:55.313][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:55.314][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.315][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:55.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:55.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.321][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.323][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.324][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.325][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.331][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.333][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.334][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.335][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.341][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.343][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.344][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.345][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.352][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:55.353][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:55.354][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.355][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.357][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:55.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:55.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.362][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:55.363][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:55.364][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.369][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.371][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:55.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:55.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.376][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-02-21 16:02:55.377][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:55.379][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.380][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.381][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-02-21 16:02:55.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:55.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.445][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.450][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.455][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:55.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.460][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.465][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.470][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:55.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:55.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:55.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.504][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.509][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:55.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.519][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.524][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:55.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.534][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:55.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:55.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:55.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:55.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.544][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:55.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:55.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.549][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:55.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:55.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.554][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:55.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:55.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.559][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:55.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:55.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:55.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:55.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:55.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:55.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:55.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:55.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:55.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:55.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.588][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:55.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:55.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:55.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:55.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.602][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.612][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.617][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.622][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:55.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:55.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.656][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.661][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.666][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:55.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.671][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.676][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.680][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.685][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:55.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:55.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.690][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:55.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:55.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:55.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:55.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.700][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-21 16:02:55.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.719][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-21 16:02:55.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:55.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:55.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:55.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.773][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.810][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.820][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:55.854][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-02-21 16:02:55.857][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:55.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:55.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:55.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:55.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.867][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:55.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:55.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.872][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:55.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:55.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.889][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.933][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.938][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.943][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:55.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.974][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.975][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.976][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.977][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:55.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:55.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:55.995][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:55.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:55.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.000][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.005][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.010][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.011][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.012][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.013][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.015][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.049][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.050][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.052][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.053][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.069][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.074][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.079][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.084][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.085][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.086][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.088][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.089][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.119][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.120][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.121][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.122][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.139][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.144][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.149][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.154][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.155][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.157][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.158][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.159][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:56.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:56.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:56.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:56.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:56.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:56.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.189][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:56.190][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:56.192][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.193][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:56.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:56.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.210][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:56.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:56.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.215][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:56.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:56.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.220][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:56.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:56.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.225][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:56.226][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:56.227][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.228][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.230][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:56.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:56.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.246][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:56.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:56.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.256][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:56.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:56.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.261][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:56.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:56.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.266][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:56.267][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:56.268][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.269][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.270][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:56.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:56.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.285][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.290][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.295][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.300][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.302][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.303][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.304][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.305][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.336][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.337][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.338][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.339][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.357][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.362][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.367][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.372][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.373][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.374][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.375][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.392][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.397][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.402][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.407][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.408][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.409][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.410][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.412][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.433][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.438][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.444][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.445][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.446][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.447][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.465][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:56.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:56.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.470][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:56.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:56.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.480][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:56.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:56.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.486][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:56.487][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:56.488][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.490][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.491][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:56.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:56.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:56.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:56.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:56.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:56.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:56.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:56.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.523][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:56.524][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:56.526][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.527][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:56.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:56.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.560][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.561][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.562][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.563][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.581][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.586][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.591][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.596][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.597][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.599][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.600][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.601][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.617][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:56.619][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:56.620][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.621][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.627][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.629][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:56.630][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.631][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.638][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.639][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:56.640][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.641][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.648][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.650][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:56.651][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.652][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.660][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.661][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:56.662][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.664][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.670][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.672][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:56.673][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.674][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.680][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.682][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:56.683][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.684][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.690][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.692][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:56.693][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.694][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.700][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:56.702][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:56.703][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.704][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.715][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:56.716][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:56.717][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.718][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.725][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:56.726][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:56.727][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.728][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.735][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.736][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:56.737][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.738][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.745][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.746][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:56.747][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.748][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.755][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.756][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:56.757][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.758][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.765][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:56.766][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:56.767][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.768][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.775][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.776][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:56.777][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.778][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.785][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.786][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:56.787][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.788][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:56.795][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:56.796][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:56.797][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:56.798][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:56.809][biodb::testThat]
biodb.INFO [2026-02-21 16:02:56.810][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-21 16:02:56.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:56.812][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:56.831][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-21 16:02:56.835][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:56.838][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:56.877][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-21 16:02:56.879][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-21 16:02:56.880][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:57.061][biodb::testThat]
biodb.INFO [2026-02-21 16:02:57.062][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-21 16:02:57.063][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:57.064][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:57.069][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:57.070][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:57.071][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:57.072][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:57.074][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-02-21 16:02:57.109][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-21 16:02:57.186][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:57.188][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:57.189][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-21 16:02:57.191][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-21 16:02:57.208][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:57.282][biodb::testThat]
biodb.INFO [2026-02-21 16:02:57.284][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-21 16:02:57.285][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:57.286][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:57.296][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-21 16:02:57.297][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:57.299][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:57.301][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-21 16:02:57.302][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-21 16:02:57.303][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:57.364][biodb::testThat]
biodb.INFO [2026-02-21 16:02:57.365][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-21 16:02:57.366][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:57.367][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:57.372][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-21 16:02:57.374][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:57.375][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:57.377][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-21 16:02:57.379][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-21 16:02:57.380][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:57.436][biodb::testThat]
biodb.INFO [2026-02-21 16:02:57.437][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-21 16:02:57.438][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:57.439][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:57.500][biodb::testThat]
biodb.INFO [2026-02-21 16:02:57.502][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-21 16:02:57.503][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:57.504][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:57.560][biodb::testThat]
biodb.INFO [2026-02-21 16:02:57.562][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:57.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:57.564][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:57.620][biodb::testThat]
biodb.INFO [2026-02-21 16:02:57.621][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:57.622][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:57.624][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-02-21 16:02:57.701][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:57.703][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:57.704][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:57.705][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:57.706][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:57.707][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:57.709][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:57.710][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:57.711][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:57.712][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:57.713][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:57.714][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:57.716][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:57.717][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:57.718][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:57.719][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:57.721][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:57.722][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:57.723][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:57.724][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:57.725][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:57.727][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:57.728][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:57.729][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:57.730][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:02:57.732][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-02-21 16:02:57.733][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:02:57.734][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:57.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:57.736][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:57.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:57.738][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:57.739][FUN] Functions in observer 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)