Back to Long Tests report for BioC 3.22

This page was generated on 2025-11-16 16:54 -0500 (Sun, 16 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4903
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: 2025-11-15 09:55 -0500 (Sat, 15 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  

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: 2025-11-15 16:01:10 -0500 (Sat, 15 Nov 2025)
EndedAt: 2025-11-15 16:02:19 -0500 (Sat, 15 Nov 2025)
EllapsedTime: 69.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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Platform: x86_64-pc-linux-gnu

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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 [2025-11-15 16:02:15.134][biodb::testContext]
biodb.INFO [2025-11-15 16:02:15.136][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-15 16:02:15.137][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-15 16:02:15.138][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-15 16:02:15.139][biodb::testContext]
biodb.INFO [2025-11-15 16:02:15.145][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-11-15 16:02:15.147][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-15 16:02:15.153][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:02:15.154][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-15 16:02:15.155][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-15 16:02:15.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.159][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-15 16:02:15.175][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-15 16:02:15.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.178][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.179][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-15 16:02:15.180][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-15 16:02:15.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.191][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-15 16:02:15.192][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-15 16:02:15.193][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-15 16:02:15.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.196][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.197][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-15 16:02:15.197][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-15 16:02:15.198][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-15 16:02:15.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.202][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-15 16:02:15.203][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-15 16:02:15.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.206][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-15 16:02:15.207][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-15 16:02:15.208][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-15 16:02:15.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.211][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-15 16:02:15.212][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-15 16:02:15.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.215][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.216][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-15 16:02:15.217][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-15 16:02:15.218][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-15 16:02:15.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.221][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-15 16:02:15.222][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-15 16:02:15.223][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-15 16:02:15.224][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-15 16:02:15.225][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-15 16:02:15.226][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-15 16:02:15.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.228][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.229][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-15 16:02:15.230][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-15 16:02:15.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.233][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-15 16:02:15.234][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-15 16:02:15.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.237][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.238][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-15 16:02:15.238][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-15 16:02:15.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.242][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-15 16:02:15.243][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-15 16:02:15.244][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-15 16:02:15.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.247][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-15 16:02:15.248][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-15 16:02:15.251][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-15 16:02:15.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.254][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-15 16:02:15.255][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-15 16:02:15.256][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-15 16:02:15.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.262][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-15 16:02:15.292][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.307][self$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[2025-11-15 16:02:15.308][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.309][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:02:15.310][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.311][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.312][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.312][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.313][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-15 16:02:15.314][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:02:15.315][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.316][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-15 16:02:15.317][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:02:15.318][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.319][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.320][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-15 16:02:15.320][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-15 16:02:15.320][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-15 16:02:15.320][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-15 16:02:15.320][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-15 16:02:15.321][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:02:15.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.323][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:02:15.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.326][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.327][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.328][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:02:15.329][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:02:15.330][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.330][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.332][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-15 16:02:15.333][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.334][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-15 16:02:15.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.336][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:02:15.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.339][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.344][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.345][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-15 16:02:15.346][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:02:15.346][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.347][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-15 16:02:15.348][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:02:15.349][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.350][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.351][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-15 16:02:15.351][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-15 16:02:15.351][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-15 16:02:15.351][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-15 16:02:15.351][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-15 16:02:15.352][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:02:15.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.355][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:02:15.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.357][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.358][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.359][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:02:15.360][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:02:15.361][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.362][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.363][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-15 16:02:15.364][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.365][self$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[2025-11-15 16:02:15.366][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.367][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:02:15.368][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.369][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.370][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.371][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.372][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-15 16:02:15.373][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:02:15.374][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.375][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-15 16:02:15.376][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:02:15.376][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.377][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.378][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.379][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:02:15.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:02:15.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.384][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.385][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:02:15.387][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:02:15.388][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.389][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.390][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-15 16:02:15.391][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.392][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-15 16:02:15.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:02:15.395][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.396][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.397][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.398][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.399][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-15 16:02:15.400][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:02:15.401][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.402][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-15 16:02:15.403][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:02:15.403][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.404][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.405][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.406][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-15 16:02:15.407][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.409][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:02:15.410][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.412][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.413][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:02:15.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:02:15.415][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.416][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.419][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:02:15.420][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.421][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.425][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.429][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.433][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.438][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.442][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.446][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.450][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.454][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.458][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.462][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.466][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.471][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.475][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.479][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.483][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.487][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.488][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-15 16:02:15.492][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-15 16:02:15.493][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-15 16:02:15.495][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-15 16:02:15.496][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-15 16:02:15.501][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-15 16:02:15.502][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-15 16:02:15.504][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-15 16:02:15.505][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-15 16:02:15.506][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-15 16:02:15.508][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-15 16:02:15.509][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-15 16:02:15.510][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-15 16:02:15.511][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-15 16:02:15.513][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-15 16:02:15.514][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-15 16:02:15.515][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-15 16:02:15.517][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-15 16:02:15.518][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-15 16:02:15.519][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-15 16:02:15.521][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-15 16:02:15.522][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-15 16:02:15.523][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-15 16:02:15.524][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-15 16:02:15.526][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-15 16:02:15.527][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-15 16:02:15.528][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-15 16:02:15.530][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-15 16:02:15.531][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-15 16:02:15.532][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-15 16:02:15.534][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-15 16:02:15.535][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-15 16:02:15.536][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-15 16:02:15.537][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-15 16:02:15.539][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-15 16:02:15.540][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-15 16:02:15.541][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-15 16:02:15.543][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-15 16:02:15.544][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-15 16:02:15.545][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-15 16:02:15.546][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-15 16:02:15.548][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-15 16:02:15.549][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-15 16:02:15.550][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-15 16:02:15.552][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-15 16:02:15.553][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-15 16:02:15.554][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-15 16:02:15.556][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-15 16:02:15.557][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-15 16:02:15.558][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-15 16:02:15.559][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-15 16:02:15.561][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-15 16:02:15.562][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-15 16:02:15.563][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-15 16:02:15.565][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-15 16:02:15.566][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-15 16:02:15.567][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-15 16:02:15.569][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-15 16:02:15.570][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-15 16:02:15.577][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-15 16:02:15.579][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-15 16:02:15.580][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-15 16:02:15.582][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-15 16:02:15.583][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-15 16:02:15.585][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-15 16:02:15.586][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-15 16:02:15.588][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-15 16:02:15.589][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-15 16:02:15.591][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-15 16:02:15.592][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-15 16:02:15.594][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-15 16:02:15.595][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-15 16:02:15.596][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-15 16:02:15.598][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-15 16:02:15.599][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-15 16:02:15.601][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-15 16:02:15.602][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-15 16:02:15.604][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-15 16:02:15.605][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-15 16:02:15.607][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-15 16:02:15.608][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-15 16:02:15.609][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-15 16:02:15.611][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-15 16:02:15.618][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-15 16:02:15.620][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-11-15 16:02:15.623][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-15 16:02:15.624][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.626][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.627][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.638][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.644][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.650][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.657][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.663][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.683][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.689][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.696][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.702][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.709][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.715][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.721][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.728][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.734][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.740][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.747][FUN] Functions in observer BiodbConfig: [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 [2025-11-15 16:02:15.748][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-11-15 16:02:15.756][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-11-15 16:02:15.769][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-11-15 16:02:15.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-15 16:02:15.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-15 16:02:15.777][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-11-15 16:02:15.786][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-11-15 16:02:15.788][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.789][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.790][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-15 16:02:15.791][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.792][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-11-15 16:02:15.793][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.795][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-15 16:02:15.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-15 16:02:15.797][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.798][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-11-15 16:02:15.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-11-15 16:02:15.800][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-11-15 16:02:15.801][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-15 16:02:15.802][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-15 16:02:15.802][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-11-15 16:02:15.802][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-11-15 16:02:15.803][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-15 16:02:15.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.806][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-15 16:02:15.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-15 16:02:15.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-15 16:02:15.809][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-15 16:02:15.809][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-11-15 16:02:15.809][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-11-15 16:02:15.810][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-15 16:02:15.811][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-15 16:02:15.812][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-15 16:02:15.813][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-15 16:02:15.819][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-11-15 16:02:15.820][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-15 16:02:15.822][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-15 16:02:15.823][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-15 16:02:15.825][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-15 16:02:15.850][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-11-15 16:02:15.865][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-11-15 16:02:15.873][biodb::testThat]
biodb.INFO [2025-11-15 16:02:15.874][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-15 16:02:15.874][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:15.875][biodb::testThat]
biodb.TRACE[2025-11-15 16:02:15.879][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[2025-11-15 16:02:15.881][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-11-15 16:02:15.884][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-11-15 16:02:15.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-15 16:02:15.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:15.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:15.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:15.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:15.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:15.907][FUN] Functions in observer BiodbConfig: [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[2025-11-15 16:02:15.918][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:15.919][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:15.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.920][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:15.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:15.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.937][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:15.938][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:15.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.940][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.965][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:15.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:15.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.969][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:15.970][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:15.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.971][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.973][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:15.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:15.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.976][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:15.977][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:15.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.979][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.980][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:15.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:15.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.984][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:15.985][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:15.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.987][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:15.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:15.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.992][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:15.993][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:15.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:15.995][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:15.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:15.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:15.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.009][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.010][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.011][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.013][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.016][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.017][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.019][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.020][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.024][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.025][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.027][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.028][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.032][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.033][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.035][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.036][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.040][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.041][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.042][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.047][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.048][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.050][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.055][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.056][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.058][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.063][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.064][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.065][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.070][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.071][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.073][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.078][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.079][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.080][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.081][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.082][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.085][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.086][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.088][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.089][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.093][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-11-15 16:02:16.094][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.096][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.097][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-11-15 16:02:16.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.184][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.188][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.192][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.196][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.199][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.203][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.229][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.233][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.236][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.240][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.247][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.255][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.258][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.262][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.266][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.269][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.273][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.303][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.310][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.314][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.318][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.344][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.348][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.351][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.355][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.359][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.363][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.366][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.370][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.374][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.378][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-15 16:02:16.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.392][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-11-15 16:02:16.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.424][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.428][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.435][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.439][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.446][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-15 16:02:16.472][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-11-15 16:02:16.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-15 16:02:16.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-15 16:02:16.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.478][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-15 16:02:16.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-15 16:02:16.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-15 16:02:16.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-15 16:02:16.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.486][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-15 16:02:16.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-15 16:02:16.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.498][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.533][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.536][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.540][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-11-15 16:02:16.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.561][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.562][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.564][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:16.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:16.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.575][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.579][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.582][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.586][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.587][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.589][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.590][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:16.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.611][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.612][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.614][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:16.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.625][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.629][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.636][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.637][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.639][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.640][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:16.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.665][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.666][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.667][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.668][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:16.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.679][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.683][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.686][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.690][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.691][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.693][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.694][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.715][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.716][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.718][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:16.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:16.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.729][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.732][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.736][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.740][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.741][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.743][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.744][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:16.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:16.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.757][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.765][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.768][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.769][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.771][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:16.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:16.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.782][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.786][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.790][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.793][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.794][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.796][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.797][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:16.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.819][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.821][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:16.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.832][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.836][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.839][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.843][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.844][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.846][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.847][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:16.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.857][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.864][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.868][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.869][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.870][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.871][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:16.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.893][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.896][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.897][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.899][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:16.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.910][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.914][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.918][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.921][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.922][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.924][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:16.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:16.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.935][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.939][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.946][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.947][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.949][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:16.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:16.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.971][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.972][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.974][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:16.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.989][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.992][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:16.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:16.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:16.996][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:17.001][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:17.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.003][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.004][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:17.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:17.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.014][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-15 16:02:17.015][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-15 16:02:17.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.017][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.020][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-11-15 16:02:17.021][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-11-15 16:02:17.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.023][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.027][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-11-15 16:02:17.028][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-11-15 16:02:17.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.030][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.033][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-15 16:02:17.035][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-15 16:02:17.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.036][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.040][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:17.041][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-11-15 16:02:17.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.043][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.047][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:17.048][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-11-15 16:02:17.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.049][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.053][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:17.054][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-11-15 16:02:17.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.056][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.060][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:17.061][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-11-15 16:02:17.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.063][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.066][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:17.067][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:17.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.069][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.073][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-15 16:02:17.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-15 16:02:17.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.076][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.079][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-15 16:02:17.081][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-15 16:02:17.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.082][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.086][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-15 16:02:17.087][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-15 16:02:17.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.089][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.093][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:17.094][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-15 16:02:17.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.095][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.099][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:17.100][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-15 16:02:17.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.102][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.106][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:17.107][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:17.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.109][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.112][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:17.113][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-11-15 16:02:17.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.119][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.123][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:17.124][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:17.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.126][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.130][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-15 16:02:17.131][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-15 16:02:17.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.132][ef$get] fields variable is a list.
biodb.INFO [2025-11-15 16:02:17.139][biodb::testThat]
biodb.INFO [2025-11-15 16:02:17.140][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-15 16:02:17.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:17.141][biodb::testThat]
biodb.DEBUG[2025-11-15 16:02:17.154][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-15 16:02:17.157][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-15 16:02:17.160][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-15 16:02:17.188][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-15 16:02:17.189][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-15 16:02:17.190][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-15 16:02:17.315][biodb::testThat]
biodb.INFO [2025-11-15 16:02:17.316][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-15 16:02:17.317][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:17.318][biodb::testThat]
biodb.TRACE[2025-11-15 16:02:17.321][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:17.322][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:17.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.323][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-15 16:02:17.329][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-11-15 16:02:17.349][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-15 16:02:17.392][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-15 16:02:17.394][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-15 16:02:17.395][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-15 16:02:17.396][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-15 16:02:17.408][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-15 16:02:17.463][biodb::testThat]
biodb.INFO [2025-11-15 16:02:17.464][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-15 16:02:17.465][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:17.466][biodb::testThat]
biodb.DEBUG[2025-11-15 16:02:17.472][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-15 16:02:17.473][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-15 16:02:17.475][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-15 16:02:17.476][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-15 16:02:17.477][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-15 16:02:17.478][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-15 16:02:17.522][biodb::testThat]
biodb.INFO [2025-11-15 16:02:17.523][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-15 16:02:17.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:17.525][biodb::testThat]
biodb.DEBUG[2025-11-15 16:02:17.530][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-11-15 16:02:17.531][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-11-15 16:02:17.532][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-11-15 16:02:17.533][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-11-15 16:02:17.535][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-11-15 16:02:17.536][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-15 16:02:17.581][biodb::testThat]
biodb.INFO [2025-11-15 16:02:17.582][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-15 16:02:17.583][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:17.584][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-15 16:02:17.634][biodb::testThat]
biodb.INFO [2025-11-15 16:02:17.635][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-15 16:02:17.636][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:17.637][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-15 16:02:17.683][biodb::testThat]
biodb.INFO [2025-11-15 16:02:17.684][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-15 16:02:17.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:17.686][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.INFO [2025-11-15 16:02:17.737][biodb::testThat]
biodb.INFO [2025-11-15 16:02:17.738][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-15 16:02:17.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-15 16:02:17.740][biodb::testThat]
Saving _problems/test_long_100_generic-43.R
biodb.TRACE[2025-11-15 16:02:17.798][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:17.799][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:17.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.801][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.802][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:17.803][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:17.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.805][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.806][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:17.807][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:17.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.809][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.810][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-15 16:02:17.811][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-15 16:02:17.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.813][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.814][ef$get] Asked field names are: description.
biodb.TRACE[2025-11-15 16:02:17.815][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-11-15 16:02:17.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.817][ef$get] fields variable is a list.
biodb.TRACE[2025-11-15 16:02:17.818][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:17.819][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-11-15 16:02:17.820][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-15 16:02:17.821][ef$get] fields variable is a list.
biodb.INFO [2025-11-15 16:02:17.822][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-15 16:02:17.824][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-11-15 16:02:17.824][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-15 16:02:17.825][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-15 16:02:17.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-15 16:02:17.833][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-15 16:02:17.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-15 16:02:17.834][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-15 16:02:17.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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 4.5.1 Patched (2025-08-23 r88802)
* 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)