Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-22 23:55 -0500 (Sat, 22 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4873
merida1macOS 12.7.6 Montereyx86_644.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" 4654
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 6/31HostnameOS / ArchCHECK
biodbHmdb 1.16.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-11-22 09:55 -0500 (Sat, 22 Nov 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_22
git_last_commit: 4102973
git_last_commit_date: 2025-10-29 11:13:48 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on nebbiolo2

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

raw results


Summary

Package: biodbHmdb
Version: 1.16.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.16.0.tar.gz
StartedAt: 2025-11-22 16:01:08 -0500 (Sat, 22 Nov 2025)
EndedAt: 2025-11-22 16:02:16 -0500 (Sat, 22 Nov 2025)
EllapsedTime: 68.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-11-22 16:02:13.261][biodb::testContext]
biodb.INFO [2025-11-22 16:02:13.263][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:02:13.264][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-22 16:02:13.265][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:02:13.266][biodb::testContext]
biodb.INFO [2025-11-22 16:02:13.272][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:02:13.274][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:02:13.281][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:02:13.282][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:02:13.283][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:02:13.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.286][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:02:13.303][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:02:13.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.306][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:02:13.307][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:02:13.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.319][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:02:13.320][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:02:13.321][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:02:13.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.324][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:02:13.325][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:02:13.326][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:02:13.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.329][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:02:13.330][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:02:13.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.334][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:02:13.335][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:02:13.336][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:02:13.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.339][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:02:13.340][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:02:13.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.343][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:02:13.344][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:02:13.345][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:02:13.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.349][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:02:13.350][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:02:13.350][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:02:13.351][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:02:13.352][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:02:13.353][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:02:13.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.357][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:02:13.358][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:02:13.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.361][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:02:13.362][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:02:13.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.364][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[2025-11-22 16:02:13.365][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:02:13.366][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:02:13.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.370][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:02:13.370][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:02:13.371][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:02:13.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.375][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:02:13.376][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:02:13.379][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:02:13.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.382][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:02:13.383][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:02:13.384][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:02:13.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.390][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:02:13.420][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.435][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:02:13.436][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.437][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:13.438][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.438][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.439][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.440][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.441][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:02:13.442][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:13.443][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.444][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:02:13.445][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:13.446][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.447][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.448][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:02:13.448][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:02:13.448][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:02:13.448][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:02:13.448][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:02:13.449][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:02:13.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.451][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:13.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.453][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.454][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.455][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.456][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:13.457][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:13.457][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.458][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.459][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:02:13.461][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.462][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:02:13.463][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.464][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:13.465][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.466][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.467][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.472][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.473][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:02:13.474][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:13.474][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.475][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:02:13.476][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:13.477][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.478][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.479][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:02:13.479][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:02:13.479][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:02:13.479][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:02:13.479][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:02:13.480][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:02:13.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.483][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:13.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.485][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.486][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.487][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:13.488][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:13.489][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.490][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.491][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:02:13.492][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.493][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:02:13.494][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.495][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:13.496][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.498][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.499][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.500][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:02:13.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:13.502][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.503][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:02:13.503][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:13.504][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.505][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.506][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.507][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:02:13.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.510][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:13.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.512][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.513][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.514][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:13.515][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:13.516][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.517][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.518][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:02:13.520][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.520][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:02:13.521][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.522][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:13.523][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.524][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.525][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.526][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.527][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:02:13.528][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:13.529][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.530][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:02:13.531][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:13.532][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.533][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.533][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.534][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:02:13.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.537][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:13.538][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.539][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.540][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.541][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:13.542][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:13.543][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.544][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.548][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:02:13.548][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.558][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[2025-11-22 16:02:13.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.583][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[2025-11-22 16:02:13.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.587][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[2025-11-22 16:02:13.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.591][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[2025-11-22 16:02:13.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.608][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[2025-11-22 16:02:13.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.612][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[2025-11-22 16:02:13.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.617][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:02:13.621][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:02:13.622][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:02:13.624][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:02:13.625][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:02:13.630][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:02:13.631][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:02:13.633][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:02:13.634][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:02:13.635][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:02:13.637][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:02:13.638][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:02:13.639][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:02:13.640][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:02:13.642][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:02:13.643][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:02:13.644][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:02:13.646][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:02:13.647][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:02:13.648][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:02:13.649][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:02:13.651][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:02:13.652][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:02:13.653][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:02:13.655][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:02:13.656][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:02:13.657][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:02:13.658][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:02:13.660][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:02:13.661][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:02:13.662][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:02:13.664][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:02:13.665][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:02:13.666][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:02:13.667][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:02:13.669][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:02:13.670][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:02:13.671][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:02:13.673][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:02:13.674][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:02:13.675][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:02:13.676][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:02:13.678][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:02:13.679][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:02:13.680][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:02:13.682][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:02:13.683][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:02:13.684][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:02:13.690][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:02:13.692][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:02:13.694][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:02:13.695][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:02:13.697][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:02:13.698][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:02:13.700][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:02:13.701][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:02:13.703][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:02:13.704][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:02:13.706][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:02:13.707][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:02:13.708][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:02:13.710][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:02:13.711][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:02:13.713][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:02:13.714][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:02:13.716][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:02:13.717][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:02:13.718][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:02:13.720][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:02:13.721][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:02:13.723][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:02:13.724][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:02:13.726][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:02:13.727][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:02:13.728][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:02:13.730][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:02:13.731][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:02:13.733][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:02:13.734][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:02:13.736][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:02:13.737][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:02:13.738][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:02:13.740][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:02:13.747][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:02:13.749][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-22 16:02:13.752][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:02:13.753][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.755][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:02:13.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.WARN [2025-11-22 16:02:13.875][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-11-22 16:02:13.883][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-11-22 16:02:13.896][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-11-22 16:02:13.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:02:13.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:13.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:13.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:13.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:13.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:13.902][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".
biodb.DEBUG[2025-11-22 16:02:13.904][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-11-22 16:02:13.912][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-11-22 16:02:13.914][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.915][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.916][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.917][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:02:13.918][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.919][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-11-22 16:02:13.920][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.921][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.922][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:02:13.923][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:02:13.924][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.925][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-11-22 16:02:13.925][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-11-22 16:02:13.926][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-11-22 16:02:13.928][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:02:13.928][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:02:13.928][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-11-22 16:02:13.928][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-11-22 16:02:13.929][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:02:13.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.932][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:02:13.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:02:13.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:02:13.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:02:13.936][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-11-22 16:02:13.936][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-11-22 16:02:13.937][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:02:13.937][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:02:13.938][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:02:13.939][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:02:13.945][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-11-22 16:02:13.946][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:02:13.948][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:02:13.949][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:02:13.951][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:02:13.975][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-11-22 16:02:13.990][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-11-22 16:02:13.997][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.998][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-22 16:02:13.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:14.000][biodb::testThat]
biodb.TRACE[2025-11-22 16:02:14.003][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-11-22 16:02:14.005][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:02:14.008][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-11-22 16:02:14.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:14.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:14.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:14.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:14.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:14.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:14.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:02:14.042][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.045][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.061][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.062][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.064][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.089][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.093][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.094][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.096][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.097][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.101][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.102][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.104][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.105][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.109][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.110][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.112][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.117][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.118][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.120][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.133][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.134][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.136][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.137][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.141][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.142][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.144][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.145][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.149][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.150][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.151][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.153][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.156][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.157][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.159][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.160][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.164][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.165][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.167][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.168][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.172][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:14.173][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:14.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.174][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:14.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:14.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.179][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.180][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.182][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.183][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.187][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.188][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.190][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.195][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.195][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.197][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.202][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.203][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.205][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.206][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.210][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:14.211][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:14.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.212][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.213][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:14.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:14.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.217][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-11-22 16:02:14.218][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.220][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.221][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-11-22 16:02:14.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.308][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.312][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.315][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.319][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.323][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.326][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:14.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.352][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.360][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.363][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.367][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.371][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:14.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.375][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.378][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.382][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.386][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.389][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.393][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:14.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:14.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:14.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:14.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.419][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:14.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:14.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.434][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.438][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.441][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.467][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.471][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.474][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.478][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.482][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.485][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.489][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:14.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:14.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.493][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:14.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:14.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.496][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:14.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:14.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.500][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-22 16:02:14.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.515][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-22 16:02:14.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:14.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.561][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.568][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:14.594][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-11-22 16:02:14.596][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:02:14.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:02:14.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.600][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:02:14.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:02:14.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.603][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:02:14.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:02:14.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.607][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:02:14.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:02:14.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.619][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.654][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.658][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.662][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-22 16:02:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.683][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.684][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.685][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:14.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:14.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.697][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.701][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.704][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.708][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.709][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.711][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:14.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.733][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.734][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.736][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:14.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.747][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.750][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.754][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.758][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.759][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.760][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.761][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:14.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.787][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.788][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.789][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:14.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.800][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.804][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.808][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.811][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.812][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.814][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.815][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:14.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.836][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.837][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.839][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.854][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.857][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.861][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.862][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.864][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.865][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:14.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:14.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.878][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.889][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.890][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.892][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.893][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:14.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:14.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.903][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.907][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.910][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.914][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.915][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.917][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.918][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:14.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.939][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.940][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.942][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.957][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.960][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.964][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.965][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.967][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.968][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:14.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.978][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.986][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.989][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.990][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.992][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.993][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:14.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.018][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.019][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.021][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.032][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:15.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:15.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.036][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:15.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:15.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.040][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:15.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:15.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.043][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:15.044][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:15.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.046][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.047][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:15.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:15.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:15.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:15.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:15.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:15.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:15.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:15.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.068][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:15.069][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:15.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.071][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:15.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:15.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.093][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.094][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.096][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.107][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.111][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.115][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.118][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.123][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.125][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.126][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.137][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:15.138][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:15.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.140][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.143][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-22 16:02:15.144][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-22 16:02:15.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.146][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.150][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.151][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-22 16:02:15.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.153][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.157][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:15.158][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:15.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.159][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.163][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:15.165][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-22 16:02:15.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.167][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.172][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:15.173][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-22 16:02:15.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.175][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.179][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.180][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-22 16:02:15.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.182][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.186][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:15.188][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-22 16:02:15.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.190][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.194][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:15.195][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:15.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.197][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.201][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:02:15.202][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:02:15.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.204][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.208][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:02:15.209][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:02:15.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.211][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.215][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.216][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:02:15.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.218][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.222][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:15.224][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:02:15.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.226][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.230][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:15.231][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:15.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.233][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.237][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:15.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:15.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.240][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.244][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:15.246][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-22 16:02:15.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.253][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.257][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:15.259][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:15.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.261][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.265][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:02:15.266][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:02:15.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.268][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:02:15.275][biodb::testThat]
biodb.INFO [2025-11-22 16:02:15.276][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-22 16:02:15.277][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:15.278][biodb::testThat]
biodb.DEBUG[2025-11-22 16:02:15.292][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-22 16:02:15.294][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-22 16:02:15.298][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-22 16:02:15.327][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-22 16:02:15.329][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-22 16:02:15.330][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-22 16:02:15.472][biodb::testThat]
biodb.INFO [2025-11-22 16:02:15.474][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-22 16:02:15.475][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:15.476][biodb::testThat]
biodb.TRACE[2025-11-22 16:02:15.479][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:15.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:15.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.482][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:15.483][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-11-22 16:02:15.513][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-22 16:02:15.560][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-22 16:02:15.562][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-22 16:02:15.563][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-22 16:02:15.565][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-22 16:02:15.577][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-22 16:02:15.640][biodb::testThat]
biodb.INFO [2025-11-22 16:02:15.641][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-22 16:02:15.642][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:15.643][biodb::testThat]
biodb.DEBUG[2025-11-22 16:02:15.650][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-22 16:02:15.651][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-22 16:02:15.653][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-22 16:02:15.654][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-22 16:02:15.655][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-22 16:02:15.656][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-22 16:02:15.708][biodb::testThat]
biodb.INFO [2025-11-22 16:02:15.709][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-22 16:02:15.711][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:15.711][biodb::testThat]
biodb.DEBUG[2025-11-22 16:02:15.716][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-22 16:02:15.717][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-22 16:02:15.718][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-22 16:02:15.720][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-22 16:02:15.721][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-22 16:02:15.722][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-22 16:02:15.771][biodb::testThat]
biodb.INFO [2025-11-22 16:02:15.772][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-22 16:02:15.773][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:15.774][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-22 16:02:15.823][biodb::testThat]
biodb.INFO [2025-11-22 16:02:15.825][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-22 16:02:15.826][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:15.826][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-22 16:02:15.868][biodb::testThat]
biodb.INFO [2025-11-22 16:02:15.869][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-22 16:02:15.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:15.871][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-22 16:02:15.916][biodb::testThat]
biodb.INFO [2025-11-22 16:02:15.917][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-22 16:02:15.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:15.919][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-11-22 16:02:15.973][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:15.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:15.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.976][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.977][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:15.978][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:15.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.979][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.980][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:15.981][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:15.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.983][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.984][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:15.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:15.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.987][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.988][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-22 16:02:15.989][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-22 16:02:15.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.991][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:15.992][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:15.993][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-22 16:02:15.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:15.995][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:02:15.996][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:02:15.997][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-11-22 16:02:15.998][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:02:15.998][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:15.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:16.000][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:16.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:16.006][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:16.007][FUN] Functions in observer 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)