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 nebbiolo2

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2026-02-21 16:01:11 -0500 (Sat, 21 Feb 2026)
EndedAt: 2026-02-21 16:02:19 -0500 (Sat, 21 Feb 2026)
EllapsedTime: 68.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2026-02-21 16:02:15.267][biodb::testContext]
biodb.INFO [2026-02-21 16:02:15.269][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:15.270][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-02-21 16:02:15.271][biodb::testContext] ********************************************************************************
biodb.INFO [2026-02-21 16:02:15.272][biodb::testContext]
biodb.INFO [2026-02-21 16:02:15.277][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:15.279][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:15.285][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:15.286][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-02-21 16:02:15.287][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-02-21 16:02:15.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.291][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-02-21 16:02:15.307][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-02-21 16:02:15.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.309][FUN] Functions in observer BiodbConfig: [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 16:02:15.310][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-02-21 16:02:15.311][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-02-21 16:02:15.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.315][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-02-21 16:02:15.315][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-02-21 16:02:15.316][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-02-21 16:02:15.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.319][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 16:02:15.320][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-02-21 16:02:15.321][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-02-21 16:02:15.322][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-02-21 16:02:15.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.325][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-02-21 16:02:15.326][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-02-21 16:02:15.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.328][FUN] Functions in observer BiodbConfig: [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 16:02:15.329][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-02-21 16:02:15.330][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-02-21 16:02:15.331][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-02-21 16:02:15.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.334][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-02-21 16:02:15.335][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-02-21 16:02:15.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.338][FUN] Functions in observer BiodbConfig: [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 16:02:15.339][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-02-21 16:02:15.340][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-02-21 16:02:15.341][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-02-21 16:02:15.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.344][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:15.345][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-02-21 16:02:15.346][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-02-21 16:02:15.347][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-02-21 16:02:15.348][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-02-21 16:02:15.349][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-02-21 16:02:15.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.351][FUN] Functions in observer BiodbConfig: [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 16:02:15.352][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-02-21 16:02:15.353][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-02-21 16:02:15.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.356][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-02-21 16:02:15.357][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-02-21 16:02:15.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.361][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-02-21 16:02:15.361][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-02-21 16:02:15.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.365][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-02-21 16:02:15.366][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-02-21 16:02:15.367][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-02-21 16:02:15.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.369][FUN] Functions in observer BiodbConfig: [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 16:02:15.370][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-02-21 16:02:15.371][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-02-21 16:02:15.376][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-02-21 16:02:15.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.379][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-02-21 16:02:15.380][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-02-21 16:02:15.381][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-02-21 16:02:15.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.387][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-02-21 16:02:15.417][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.437][self$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 16:02:15.438][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.439][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:15.439][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.440][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.441][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.442][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.443][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:15.444][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:15.445][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.446][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-02-21 16:02:15.447][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:15.448][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.449][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.449][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:15.449][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:15.449][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:15.449][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:15.449][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:15.450][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:15.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.453][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:15.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.456][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.456][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.457][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:15.458][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:15.459][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.460][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.461][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-02-21 16:02:15.463][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.464][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:15.465][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.465][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:15.466][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.467][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.468][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.469][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.470][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:15.471][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:15.472][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.473][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-02-21 16:02:15.474][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:15.475][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.476][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.476][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:15.476][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-02-21 16:02:15.476][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-02-21 16:02:15.476][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-02-21 16:02:15.476][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-02-21 16:02:15.477][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:15.478][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.479][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.480][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:15.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.483][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.484][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:15.485][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:15.486][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.487][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.488][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-02-21 16:02:15.490][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.491][self$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 16:02:15.492][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.492][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:15.493][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.494][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.495][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.496][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.497][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-02-21 16:02:15.498][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:15.499][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.500][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-02-21 16:02:15.501][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:15.502][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.503][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.503][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.504][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:15.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.507][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:15.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.510][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.510][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.511][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:15.512][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:15.513][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.514][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.515][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-02-21 16:02:15.517][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.518][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-02-21 16:02:15.518][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:15.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.523][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.524][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-02-21 16:02:15.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:15.526][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.527][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-02-21 16:02:15.528][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:15.529][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.530][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.530][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.531][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-02-21 16:02:15.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.534][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:15.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.537][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.537][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.538][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:15.539][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:15.540][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.541][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.544][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:15.545][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.546][FUN] Functions in observer BiodbConfig: [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 16:02:15.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.549][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 16:02:15.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.550][FUN] Functions in observer BiodbConfig: [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 16:02:15.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.553][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 16:02:15.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.554][FUN] Functions in observer BiodbConfig: [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 16:02:15.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.557][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 16:02:15.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.558][FUN] Functions in observer BiodbConfig: [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 16:02:15.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.561][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 16:02:15.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.563][FUN] Functions in observer BiodbConfig: [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 16:02:15.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.565][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 16:02:15.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.567][FUN] Functions in observer BiodbConfig: [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 16:02:15.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.569][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 16:02:15.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.571][FUN] Functions in observer BiodbConfig: [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 16:02:15.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.573][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 16:02:15.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.575][FUN] Functions in observer BiodbConfig: [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 16:02:15.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.577][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 16:02:15.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.579][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 16:02:15.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.582][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 16:02:15.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.583][FUN] Functions in observer BiodbConfig: [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 16:02:15.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.586][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 16:02:15.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.587][FUN] Functions in observer BiodbConfig: [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 16:02:15.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.590][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 16:02:15.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.591][FUN] Functions in observer BiodbConfig: [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 16:02:15.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.594][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 16:02:15.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.596][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 16:02:15.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.598][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 16:02:15.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.600][FUN] Functions in observer BiodbConfig: [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 16:02:15.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.602][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 16:02:15.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.604][FUN] Functions in observer BiodbConfig: [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 16:02:15.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-02-21 16:02:15.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.608][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 16:02:15.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.610][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 16:02:15.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.613][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-02-21 16:02:15.617][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-02-21 16:02:15.618][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-02-21 16:02:15.620][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-02-21 16:02:15.621][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-02-21 16:02:15.622][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:15.624][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:15.625][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:15.626][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-02-21 16:02:15.627][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:15.633][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:15.634][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-02-21 16:02:15.635][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-02-21 16:02:15.643][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-02-21 16:02:15.645][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-02-21 16:02:15.647][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:15.648][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-02-21 16:02:15.650][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-02-21 16:02:15.651][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-02-21 16:02:15.653][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-02-21 16:02:15.655][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-02-21 16:02:15.656][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-02-21 16:02:15.658][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-02-21 16:02:15.659][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-02-21 16:02:15.661][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-02-21 16:02:15.662][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-02-21 16:02:15.664][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-02-21 16:02:15.665][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-02-21 16:02:15.667][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-02-21 16:02:15.668][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-02-21 16:02:15.670][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-02-21 16:02:15.672][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-02-21 16:02:15.673][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-02-21 16:02:15.675][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-02-21 16:02:15.676][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-02-21 16:02:15.678][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-02-21 16:02:15.679][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-02-21 16:02:15.680][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-02-21 16:02:15.682][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-02-21 16:02:15.683][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-02-21 16:02:15.685][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-02-21 16:02:15.686][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-02-21 16:02:15.688][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-02-21 16:02:15.689][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-02-21 16:02:15.691][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-02-21 16:02:15.692][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-02-21 16:02:15.693][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-02-21 16:02:15.695][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-02-21 16:02:15.696][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-02-21 16:02:15.698][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-02-21 16:02:15.699][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-02-21 16:02:15.701][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-02-21 16:02:15.702][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-02-21 16:02:15.704][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-02-21 16:02:15.705][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-02-21 16:02:15.707][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-02-21 16:02:15.708][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-02-21 16:02:15.709][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-02-21 16:02:15.711][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-02-21 16:02:15.712][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-02-21 16:02:15.714][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-02-21 16:02:15.715][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-02-21 16:02:15.717][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-02-21 16:02:15.718][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-02-21 16:02:15.719][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-02-21 16:02:15.721][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-02-21 16:02:15.722][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-02-21 16:02:15.724][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-02-21 16:02:15.725][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-02-21 16:02:15.727][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-02-21 16:02:15.728][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-02-21 16:02:15.729][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-02-21 16:02:15.731][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-02-21 16:02:15.732][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-02-21 16:02:15.734][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-02-21 16:02:15.735][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-02-21 16:02:15.737][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-02-21 16:02:15.738][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-02-21 16:02:15.739][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-02-21 16:02:15.741][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-02-21 16:02:15.742][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-02-21 16:02:15.744][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-02-21 16:02:15.745][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-02-21 16:02:15.752][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-02-21 16:02:15.754][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-02-21 16:02:15.757][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-02-21 16:02:15.758][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.759][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 16:02:15.760][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.761][FUN] Functions in observer BiodbConfig: [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 16:02:15.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.770][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 16:02:15.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.772][FUN] Functions in observer BiodbConfig: [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 16:02:15.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.776][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 16:02:15.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.778][FUN] Functions in observer BiodbConfig: [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 16:02:15.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.783][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 16:02:15.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.784][FUN] Functions in observer BiodbConfig: [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 16:02:15.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.789][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 16:02:15.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.791][FUN] Functions in observer BiodbConfig: [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 16:02:15.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.795][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 16:02:15.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.797][FUN] Functions in observer BiodbConfig: [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 16:02:15.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.802][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 16:02:15.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.804][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 16:02:15.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.808][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 16:02:15.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.810][FUN] Functions in observer BiodbConfig: [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 16:02:15.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.815][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 16:02:15.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.817][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 16:02:15.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.821][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 16:02:15.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.823][FUN] Functions in observer BiodbConfig: [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 16:02:15.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.828][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 16:02:15.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.834][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 16:02:15.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.836][FUN] Functions in observer BiodbConfig: [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 16:02:15.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.840][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 16:02:15.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.847][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 16:02:15.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.863][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 16:02:15.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.864][FUN] Functions in observer BiodbConfig: [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 16:02:15.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.868][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 16:02:15.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.870][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 16:02:15.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.874][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 16:02:15.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2026-02-21 16:02:15.877][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2026-02-21 16:02:15.885][private$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 16:02:15.898][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2026-02-21 16:02:15.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-02-21 16:02:15.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:15.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:15.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:15.902][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 16:02:15.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:15.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-02-21 16:02:15.905][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2026-02-21 16:02:15.914][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2026-02-21 16:02:15.916][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.917][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.918][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.919][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-02-21 16:02:15.920][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.921][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2026-02-21 16:02:15.922][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.923][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.923][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2026-02-21 16:02:15.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-02-21 16:02:15.925][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.926][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2026-02-21 16:02:15.927][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2026-02-21 16:02:15.928][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2026-02-21 16:02:15.929][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-02-21 16:02:15.930][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-02-21 16:02:15.930][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2026-02-21 16:02:15.930][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2026-02-21 16:02:15.931][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-02-21 16:02:15.932][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.934][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-02-21 16:02:15.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-02-21 16:02:15.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-02-21 16:02:15.936][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-02-21 16:02:15.937][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2026-02-21 16:02:15.937][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2026-02-21 16:02:15.938][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-02-21 16:02:15.939][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-02-21 16:02:15.940][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-02-21 16:02:15.941][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-02-21 16:02:15.946][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2026-02-21 16:02:15.948][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-02-21 16:02:15.949][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-02-21 16:02:15.951][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-02-21 16:02:15.952][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-02-21 16:02:15.973][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2026-02-21 16:02:15.987][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2026-02-21 16:02:15.995][biodb::testThat]
biodb.INFO [2026-02-21 16:02:15.996][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-02-21 16:02:15.997][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:15.998][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:16.002][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2026-02-21 16:02:16.003][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2026-02-21 16:02:16.007][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2026-02-21 16:02:16.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-02-21 16:02:16.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:16.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:16.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:16.029][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 16:02:16.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:16.030][FUN] Functions in observer BiodbConfig: [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 16:02:16.042][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.044][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.045][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.061][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.062][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.063][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.064][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.097][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.101][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.102][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.103][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.104][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.105][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.109][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.110][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.111][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.112][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.113][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.117][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.118][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.119][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.120][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.125][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.126][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.127][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.128][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.132][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.133][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.134][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.135][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.136][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.140][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.141][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.142][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.143][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.144][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.148][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.149][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.150][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.151][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.152][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.156][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.157][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.158][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.158][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.160][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.163][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.164][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.165][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.166][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.167][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.171][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:16.172][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:16.173][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.174][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:16.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:16.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.179][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.180][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.181][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.181][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.186][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.187][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.188][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.189][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.194][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.195][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.196][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.197][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.202][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.203][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.204][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.205][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.206][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.210][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:16.211][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:16.212][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.212][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.214][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:16.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:16.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.218][ef$get] Asked field names are: super.class.
biodb.TRACE[2026-02-21 16:02:16.219][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.219][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.220][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.222][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2026-02-21 16:02:16.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.270][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.274][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.278][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.281][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.285][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:16.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.314][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.318][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.321][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.329][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.332][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.340][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.343][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.347][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.351][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.354][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.362][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:16.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:16.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:16.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:16.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:16.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:16.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.391][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.398][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.401][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.427][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.431][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.434][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.438][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.442][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.445][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.449][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:16.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:16.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.453][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:16.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:16.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.456][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:16.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:16.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.460][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-21 16:02:16.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.464][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.475][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2026-02-21 16:02:16.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:16.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.513][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.517][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.524][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:16.589][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2026-02-21 16:02:16.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:16.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-02-21 16:02:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-02-21 16:02:16.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:16.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-02-21 16:02:16.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:16.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-02-21 16:02:16.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.615][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.646][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.650][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.653][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2026-02-21 16:02:16.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.674][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.675][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.676][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.677][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:16.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:16.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.688][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.692][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.696][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.700][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.701][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.701][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.702][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.703][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:16.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.725][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.726][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.727][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.727][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:16.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.739][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.743][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.746][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.750][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.755][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.756][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.757][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.758][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:16.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.779][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.780][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.781][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.782][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:16.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.793][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.797][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.805][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.806][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.806][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.807][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.808][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:16.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.830][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.831][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.832][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.833][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:16.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:16.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.844][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.848][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.851][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.855][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.856][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.857][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.858][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.859][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:16.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:16.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.869][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.880][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.881][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.882][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.883][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.884][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:16.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:16.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.894][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.898][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.902][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.905][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.906][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.907][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.908][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.909][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:16.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.934][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.935][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.936][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.937][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:16.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.948][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.952][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.956][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.960][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.961][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.961][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.962][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.963][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.974][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.978][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.981][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.985][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.986][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.987][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.988][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.989][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:16.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:16.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:16.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.010][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.011][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.012][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.013][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.024][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:17.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:17.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.028][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:17.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:17.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.032][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:17.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:17.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.035][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:17.036][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:17.037][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.038][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.039][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:17.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:17.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:17.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:17.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:17.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:17.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:17.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:17.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.060][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:17.061][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:17.062][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.063][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:17.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:17.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.089][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.090][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.091][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.092][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.103][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.107][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.110][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.114][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.115][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.116][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.117][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.118][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.128][ef$get] Asked field names are: accession.
biodb.TRACE[2026-02-21 16:02:17.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-02-21 16:02:17.130][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.131][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.134][ef$get] Asked field names are: average.mass.
biodb.TRACE[2026-02-21 16:02:17.135][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2026-02-21 16:02:17.136][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.137][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.141][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.142][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-02-21 16:02:17.143][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.144][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.148][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2026-02-21 16:02:17.149][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2026-02-21 16:02:17.149][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.150][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.154][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:17.155][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2026-02-21 16:02:17.156][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.157][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.161][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:17.162][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2026-02-21 16:02:17.162][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.163][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.167][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.168][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2026-02-21 16:02:17.169][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.170][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.174][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:17.175][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2026-02-21 16:02:17.176][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.176][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.180][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:17.181][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:17.182][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.183][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.187][ef$get] Asked field names are: formula.
biodb.TRACE[2026-02-21 16:02:17.188][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-02-21 16:02:17.189][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.190][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-02-21 16:02:17.194][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-02-21 16:02:17.195][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.196][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.200][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.201][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-02-21 16:02:17.202][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.203][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.206][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:17.207][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2026-02-21 16:02:17.208][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.209][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.213][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:17.214][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2026-02-21 16:02:17.215][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.216][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.219][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:17.220][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:17.221][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.222][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.226][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:17.227][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2026-02-21 16:02:17.228][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.229][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.237][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:17.238][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:17.238][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.239][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.243][ef$get] Asked field names are: smiles.
biodb.TRACE[2026-02-21 16:02:17.244][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2026-02-21 16:02:17.245][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.246][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:17.252][biodb::testThat]
biodb.INFO [2026-02-21 16:02:17.253][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-02-21 16:02:17.254][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:17.255][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:17.268][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-21 16:02:17.270][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:17.273][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:17.300][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-21 16:02:17.301][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-21 16:02:17.302][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:17.428][biodb::testThat]
biodb.INFO [2026-02-21 16:02:17.429][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-02-21 16:02:17.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:17.431][biodb::testThat]
biodb.TRACE[2026-02-21 16:02:17.434][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:17.435][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:17.436][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.437][ef$get] fields variable is a list.
biodb.DEBUG[2026-02-21 16:02:17.438][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2026-02-21 16:02:17.458][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-21 16:02:17.501][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:17.502][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:17.504][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-21 16:02:17.505][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-21 16:02:17.520][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:17.570][biodb::testThat]
biodb.INFO [2026-02-21 16:02:17.571][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-02-21 16:02:17.572][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:17.573][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:17.580][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-21 16:02:17.580][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:17.582][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:17.583][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-21 16:02:17.584][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-21 16:02:17.585][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:17.625][biodb::testThat]
biodb.INFO [2026-02-21 16:02:17.626][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-02-21 16:02:17.627][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:17.627][biodb::testThat]
biodb.DEBUG[2026-02-21 16:02:17.631][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2026-02-21 16:02:17.632][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2026-02-21 16:02:17.633][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2026-02-21 16:02:17.635][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2026-02-21 16:02:17.636][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2026-02-21 16:02:17.637][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:17.680][biodb::testThat]
biodb.INFO [2026-02-21 16:02:17.681][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-02-21 16:02:17.682][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:17.683][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:17.723][biodb::testThat]
biodb.INFO [2026-02-21 16:02:17.724][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-02-21 16:02:17.725][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:17.726][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:17.770][biodb::testThat]
biodb.INFO [2026-02-21 16:02:17.771][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:17.772][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:17.773][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2026-02-21 16:02:17.813][biodb::testThat]
biodb.INFO [2026-02-21 16:02:17.814][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-02-21 16:02:17.815][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-02-21 16:02:17.816][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2026-02-21 16:02:17.869][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:17.870][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:17.871][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.872][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.873][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:17.874][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:17.875][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.875][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.876][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:17.877][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:17.878][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.879][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.880][ef$get] Asked field names are: name.
biodb.TRACE[2026-02-21 16:02:17.881][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-02-21 16:02:17.882][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.883][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.884][ef$get] Asked field names are: description.
biodb.TRACE[2026-02-21 16:02:17.885][ef$get] Realnames of fields are: description.
biodb.TRACE[2026-02-21 16:02:17.886][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.887][ef$get] fields variable is a list.
biodb.TRACE[2026-02-21 16:02:17.888][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:17.888][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2026-02-21 16:02:17.889][ef$get] 1 fields were returned.
biodb.TRACE[2026-02-21 16:02:17.890][ef$get] fields variable is a list.
biodb.INFO [2026-02-21 16:02:17.891][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-02-21 16:02:17.892][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2026-02-21 16:02:17.893][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-02-21 16:02:17.894][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-02-21 16:02:17.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-02-21 16:02:17.896][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-02-21 16:02:17.896][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 16:02:17.897][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-02-21 16:02:17.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 8 | WARN 2 | SKIP 1 | PASS 103 ]

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

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

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

'R CMD check' output

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


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

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

Installation output

biodbHmdb.Rcheck/00install.out

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