Back to Long Tests report for BioC 3.22

This page was generated on 2025-08-16 23:55 -0400 (Sat, 16 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
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 6/29HostnameOS / ArchCHECK
biodbHmdb 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-16 09:55 -0400 (Sat, 16 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: fa89c02
git_last_commit_date: 2025-07-24 10:45:35 -0400 (Thu, 24 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on nebbiolo2

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

raw results


Summary

Package: biodbHmdb
Version: 1.15.1
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_1.15.1.tar.gz
StartedAt: 2025-08-16 16:01:10 -0400 (Sat, 16 Aug 2025)
EndedAt: 2025-08-16 16:02:13 -0400 (Sat, 16 Aug 2025)
EllapsedTime: 63.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbHmdb' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-08-16 16:02:10.169][biodb::testContext]
biodb.INFO [2025-08-16 16:02:10.171][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:02:10.172][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-08-16 16:02:10.173][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-16 16:02:10.174][biodb::testContext]
biodb.INFO [2025-08-16 16:02:10.179][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:02:10.181][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-16 16:02:10.188][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:10.189][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-16 16:02:10.190][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.193][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-16 16:02:10.210][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.212][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.213][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-16 16:02:10.214][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.218][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-16 16:02:10.218][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-16 16:02:10.219][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-16 16:02:10.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.222][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.223][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-16 16:02:10.224][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-16 16:02:10.225][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.228][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-16 16:02:10.229][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-16 16:02:10.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.231][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.232][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-16 16:02:10.233][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-16 16:02:10.234][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-16 16:02:10.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.237][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-16 16:02:10.238][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.241][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[2025-08-16 16:02:10.242][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-16 16:02:10.243][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-16 16:02:10.244][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-16 16:02:10.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.247][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:02:10.248][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-16 16:02:10.249][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-16 16:02:10.250][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-16 16:02:10.251][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-16 16:02:10.252][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-16 16:02:10.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.254][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[2025-08-16 16:02:10.255][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-16 16:02:10.256][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-16 16:02:10.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.259][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-16 16:02:10.260][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-16 16:02:10.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.263][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.264][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-16 16:02:10.265][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-16 16:02:10.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.268][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-16 16:02:10.269][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-16 16:02:10.270][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-16 16:02:10.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.272][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.273][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-16 16:02:10.274][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-16 16:02:10.278][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-16 16:02:10.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.281][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-16 16:02:10.282][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-16 16:02:10.283][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-16 16:02:10.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.291][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.294][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-16 16:02:10.325][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.340][self$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[2025-08-16 16:02:10.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.342][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.342][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.343][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.344][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.346][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:02:10.347][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.348][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.349][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-16 16:02:10.350][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.351][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.352][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.353][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:10.353][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:02:10.353][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:02:10.353][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:02:10.353][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:02:10.354][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:10.355][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.359][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.360][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.361][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.361][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.362][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.363][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.364][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-16 16:02:10.366][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.367][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:02:10.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.369][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.370][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.371][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.373][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:02:10.374][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.375][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.376][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-16 16:02:10.377][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.378][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.379][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.380][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:10.380][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-16 16:02:10.380][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-16 16:02:10.380][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-16 16:02:10.380][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-16 16:02:10.381][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:10.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.383][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.387][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.388][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.389][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.390][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.391][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-16 16:02:10.393][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.394][self$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[2025-08-16 16:02:10.395][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.399][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.399][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.400][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-16 16:02:10.401][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.402][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.403][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-16 16:02:10.404][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.405][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.406][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.407][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.408][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:10.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.413][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.414][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.415][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.416][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.416][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.417][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.418][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-16 16:02:10.420][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.421][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-16 16:02:10.422][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.424][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.425][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.426][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.427][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-16 16:02:10.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.429][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.430][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-16 16:02:10.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.432][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.434][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.435][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-16 16:02:10.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.440][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.441][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.442][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.443][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.443][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.444][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.453][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:10.453][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.454][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[2025-08-16 16:02:10.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.458][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[2025-08-16 16:02:10.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.462][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[2025-08-16 16:02:10.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.467][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.471][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[2025-08-16 16:02:10.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.475][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[2025-08-16 16:02:10.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.479][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[2025-08-16 16:02:10.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.483][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[2025-08-16 16:02:10.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.487][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[2025-08-16 16:02:10.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.492][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.500][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.508][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.516][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-16 16:02:10.521][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-16 16:02:10.526][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-16 16:02:10.527][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-16 16:02:10.528][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-16 16:02:10.530][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-16 16:02:10.531][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:02:10.532][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-16 16:02:10.533][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-16 16:02:10.535][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-16 16:02:10.536][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:02:10.537][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:02:10.539][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-16 16:02:10.540][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-16 16:02:10.541][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-16 16:02:10.542][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-16 16:02:10.544][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:02:10.545][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-16 16:02:10.546][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-16 16:02:10.548][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-16 16:02:10.549][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-16 16:02:10.550][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-16 16:02:10.551][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-16 16:02:10.553][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-16 16:02:10.554][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-16 16:02:10.555][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-16 16:02:10.557][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-16 16:02:10.558][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-16 16:02:10.559][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-16 16:02:10.561][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-16 16:02:10.562][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-16 16:02:10.563][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-16 16:02:10.564][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-16 16:02:10.566][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-16 16:02:10.567][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-16 16:02:10.568][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-16 16:02:10.569][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-16 16:02:10.571][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-16 16:02:10.572][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-16 16:02:10.573][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-16 16:02:10.575][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-16 16:02:10.576][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-16 16:02:10.577][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-16 16:02:10.578][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-16 16:02:10.580][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-16 16:02:10.581][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-16 16:02:10.582][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-16 16:02:10.584][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-16 16:02:10.585][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-16 16:02:10.586][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-16 16:02:10.587][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-16 16:02:10.589][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-16 16:02:10.590][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-16 16:02:10.591][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-16 16:02:10.593][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-16 16:02:10.594][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-16 16:02:10.595][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-16 16:02:10.596][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-16 16:02:10.598][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-16 16:02:10.599][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-16 16:02:10.600][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-16 16:02:10.602][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-16 16:02:10.603][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-16 16:02:10.604][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-16 16:02:10.605][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-16 16:02:10.607][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-16 16:02:10.608][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-16 16:02:10.609][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-16 16:02:10.611][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-16 16:02:10.616][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-16 16:02:10.617][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-16 16:02:10.618][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-16 16:02:10.620][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-16 16:02:10.621][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-16 16:02:10.622][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-16 16:02:10.624][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-16 16:02:10.625][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-16 16:02:10.626][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-16 16:02:10.627][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-16 16:02:10.629][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-16 16:02:10.630][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-16 16:02:10.631][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-16 16:02:10.633][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-16 16:02:10.634][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-16 16:02:10.639][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-16 16:02:10.641][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-16 16:02:10.644][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-16 16:02:10.645][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.646][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.647][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.656][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.662][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.668][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.673][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.679][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.685][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.691][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.696][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[2025-08-16 16:02:10.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.702][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[2025-08-16 16:02:10.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.708][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.714][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.719][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.735][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.742][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.749][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.755][FUN] Functions in observer BiodbConfig: [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 [2025-08-16 16:02:10.757][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.WARN [2025-08-16 16:02:10.770][private$checkKey] Key persistent.cache.impl is deprecated. Persistent cache is now handled by the fscache CRAN package. This field is now useless.
biodb.DEBUG[2025-08-16 16:02:10.785][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-16 16:02:10.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-16 16:02:10.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.806][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.807][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-08-16 16:02:10.817][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-08-16 16:02:10.820][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.821][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.822][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.823][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-16 16:02:10.824][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.825][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-08-16 16:02:10.826][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.827][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.828][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-16 16:02:10.829][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-16 16:02:10.830][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.831][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-08-16 16:02:10.832][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-08-16 16:02:10.833][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-08-16 16:02:10.834][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-16 16:02:10.835][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-16 16:02:10.835][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-08-16 16:02:10.835][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-08-16 16:02:10.837][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-16 16:02:10.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.838][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.839][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-16 16:02:10.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-16 16:02:10.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-16 16:02:10.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-16 16:02:10.843][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-08-16 16:02:10.843][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-08-16 16:02:10.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-16 16:02:10.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-16 16:02:10.846][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-16 16:02:10.847][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-16 16:02:10.853][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-08-16 16:02:10.855][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-16 16:02:10.856][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-16 16:02:10.858][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-16 16:02:10.859][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-16 16:02:10.881][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-08-16 16:02:10.897][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-08-16 16:02:10.904][biodb::testThat]
biodb.INFO [2025-08-16 16:02:10.905][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-16 16:02:10.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:10.907][biodb::testThat]
biodb.TRACE[2025-08-16 16:02:10.911][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[2025-08-16 16:02:10.913][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-08-16 16:02:10.916][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-08-16 16:02:10.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-16 16:02:10.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:10.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:10.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:10.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:10.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:10.942][FUN] Functions in observer BiodbConfig: [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[2025-08-16 16:02:10.953][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:10.954][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:10.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:10.956][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:10.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:10.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:10.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:10.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:10.972][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:10.973][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:10.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:10.975][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.007][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.011][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.012][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.014][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.015][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.019][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.020][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.022][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.023][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.027][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.028][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.029][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.034][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.035][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.037][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.042][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.043][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.045][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.046][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.050][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.051][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.052][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.054][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.057][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.058][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.060][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.061][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.065][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.066][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.068][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.069][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.073][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.074][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.075][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.077][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.080][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.081][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.083][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.084][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.088][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.089][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.091][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.096][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.097][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.098][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.103][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.104][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.106][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.111][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.112][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.114][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.115][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.119][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.120][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.121][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.126][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.130][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-08-16 16:02:11.131][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.132][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.134][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-08-16 16:02:11.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.178][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.182][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.186][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.190][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.193][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.197][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.230][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.234][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.237][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.252][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.255][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.259][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.263][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.266][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.270][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.274][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.303][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.307][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.310][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.336][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.340][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.343][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.347][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.351][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.354][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.358][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.362][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.366][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.369][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-16 16:02:11.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.418][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-08-16 16:02:11.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.456][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.460][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.467][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:02:11.493][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-08-16 16:02:11.495][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:02:11.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:02:11.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.499][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-16 16:02:11.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-16 16:02:11.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.502][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-16 16:02:11.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-16 16:02:11.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.506][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-16 16:02:11.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-16 16:02:11.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.518][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.552][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.556][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.559][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-08-16 16:02:11.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.580][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.581][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.582][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:11.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:11.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.594][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.597][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.601][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.605][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.606][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.607][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.608][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:11.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.629][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.630][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.632][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:11.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.643][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.647][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.650][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.654][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.655][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.657][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.661][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:11.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.682][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.683][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.685][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:11.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.696][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.700][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.704][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.707][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.708][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.710][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.732][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.733][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.735][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:11.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:11.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.745][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.749][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.753][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.756][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.757][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.759][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.760][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:11.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:11.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.770][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.777][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.781][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.782][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.784][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:11.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:11.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.798][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.802][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.806][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.809][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.810][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.812][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.813][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:11.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.834][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.835][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.836][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:11.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.847][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.851][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.858][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.859][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.861][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.862][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:11.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.872][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.883][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.884][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.886][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.887][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:11.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.896][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.904][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.907][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.908][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.910][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.911][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:11.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.928][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.932][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.936][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.937][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.938][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.939][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:11.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:11.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.960][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.961][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.963][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:11.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:11.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.984][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.985][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.987][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.988][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:11.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:11.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:11.998][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:11.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.002][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.005][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.009][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.010][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.012][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.013][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.022][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-16 16:02:12.023][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-16 16:02:12.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.025][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.029][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.030][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-16 16:02:12.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.032][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.035][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.036][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-08-16 16:02:12.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.042][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.045][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.046][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-16 16:02:12.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.048][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.052][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.053][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-08-16 16:02:12.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.054][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.058][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.059][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-08-16 16:02:12.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.061][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.065][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.066][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-08-16 16:02:12.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.067][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.071][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.072][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-08-16 16:02:12.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.074][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.077][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:12.078][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:12.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.080][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.084][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-16 16:02:12.085][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-16 16:02:12.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.086][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.090][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-16 16:02:12.091][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-16 16:02:12.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.093][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.096][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.097][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-16 16:02:12.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.103][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.104][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-16 16:02:12.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.106][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.109][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.110][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-16 16:02:12.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.112][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.116][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.117][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.119][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.122][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.123][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-08-16 16:02:12.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.125][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.129][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.130][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.131][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.135][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-16 16:02:12.136][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-16 16:02:12.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.138][ef$get] fields variable is a list.
biodb.INFO [2025-08-16 16:02:12.144][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.145][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-16 16:02:12.146][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.146][biodb::testThat]
biodb.DEBUG[2025-08-16 16:02:12.163][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-16 16:02:12.166][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:12.168][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:12.195][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-16 16:02:12.197][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-16 16:02:12.197][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-16 16:02:12.232][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.233][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-16 16:02:12.234][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.235][biodb::testThat]
biodb.TRACE[2025-08-16 16:02:12.237][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.238][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.240][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-16 16:02:12.241][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-08-16 16:02:12.260][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-16 16:02:12.308][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:12.310][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:12.311][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-16 16:02:12.312][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-16 16:02:12.324][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-16 16:02:12.346][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.347][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-16 16:02:12.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.349][biodb::testThat]
biodb.DEBUG[2025-08-16 16:02:12.355][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-16 16:02:12.356][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:12.358][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:12.359][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-16 16:02:12.360][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-16 16:02:12.361][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-16 16:02:12.373][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.374][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-16 16:02:12.375][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.376][biodb::testThat]
biodb.DEBUG[2025-08-16 16:02:12.379][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-08-16 16:02:12.380][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-08-16 16:02:12.381][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-08-16 16:02:12.382][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-08-16 16:02:12.383][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-08-16 16:02:12.384][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.INFO [2025-08-16 16:02:12.399][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.400][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-16 16:02:12.401][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.402][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.414][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.415][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-16 16:02:12.416][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.417][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.429][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.430][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-16 16:02:12.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.431][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.443][biodb::testThat]
biodb.INFO [2025-08-16 16:02:12.444][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-16 16:02:12.445][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-16 16:02:12.446][biodb::testThat]
biodb.TRACE[2025-08-16 16:02:12.470][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.471][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.472][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.473][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:12.474][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:12.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.476][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.477][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.478][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.480][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.481][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-16 16:02:12.482][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-16 16:02:12.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.484][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.484][ef$get] Asked field names are: description.
biodb.TRACE[2025-08-16 16:02:12.485][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-08-16 16:02:12.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.487][ef$get] fields variable is a list.
biodb.TRACE[2025-08-16 16:02:12.488][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.489][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-08-16 16:02:12.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-16 16:02:12.491][ef$get] fields variable is a list.
biodb.INFO [2025-08-16 16:02:12.492][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-16 16:02:12.493][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-08-16 16:02:12.494][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-16 16:02:12.494][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-16 16:02:12.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-16 16:02:12.496][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-16 16:02:12.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-16 16:02:12.501][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-16 16:02:12.502][FUN] Functions in observer 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 0 | PASS 103 ]

══ 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 0 | 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_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.15.1’
* 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:
   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 0 | 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 ‘1.15.1’
** 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)