Back to Long Tests report for BioC 3.20

This page was generated on 2024-07-06 23:55 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
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 8/32HostnameOS / ArchCHECK
biodbHmdb 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-06 09:55 -0400 (Sat, 06 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: c3d59a4
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  WARNINGS  
palomino6Windows Server 2022 Datacenter / x64  WARNINGS  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

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: 1.11.0
Command: /home/biocbuild/bbs-3.20-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_1.11.0.tar.gz
StartedAt: 2024-07-06 16:02:34 -0400 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 16:04:09 -0400 (Sat, 06 Jul 2024)
EllapsedTime: 95.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 2

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-07-06 16:03:44.016][biodb::testContext]
biodb.INFO [2024-07-06 16:03:44.018][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:03:44.019][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-06 16:03:44.019][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-06 16:03:44.020][biodb::testContext]
biodb.INFO [2024-07-06 16:03:44.027][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:03:44.028][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-06 16:03:44.035][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:03:44.036][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-06 16:03:44.037][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-06 16:03:44.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.041][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-06 16:03:44.057][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-06 16:03:44.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.060][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.061][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-06 16:03:44.062][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-06 16:03:44.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.065][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-06 16:03:44.066][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-06 16:03:44.067][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-06 16:03:44.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.069][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.070][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-06 16:03:44.071][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-06 16:03:44.072][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-06 16:03:44.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.075][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-06 16:03:44.076][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-06 16:03:44.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.078][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.079][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-06 16:03:44.080][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-06 16:03:44.081][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-06 16:03:44.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.084][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-06 16:03:44.085][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-06 16:03:44.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.087][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.088][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-06 16:03:44.089][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-06 16:03:44.090][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-06 16:03:44.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.093][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:03:44.094][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-06 16:03:44.095][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-06 16:03:44.096][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-06 16:03:44.097][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-06 16:03:44.097][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-06 16:03:44.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.100][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.101][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-06 16:03:44.102][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-06 16:03:44.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.105][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-06 16:03:44.106][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-06 16:03:44.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.108][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.109][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-06 16:03:44.110][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-06 16:03:44.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.113][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-06 16:03:44.114][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:03:44.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.116][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.117][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-06 16:03:44.118][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-06 16:03:44.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.121][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-06 16:03:44.122][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-06 16:03:44.126][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-06 16:03:44.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.129][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-06 16:03:44.130][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-06 16:03:44.131][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-06 16:03:44.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.137][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-06 16:03:44.174][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.188][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-06 16:03:44.189][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.190][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:03:44.191][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.191][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.192][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.193][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.194][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:03:44.195][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:03:44.196][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.197][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-06 16:03:44.198][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:03:44.199][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.199][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.200][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:03:44.200][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:03:44.200][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:03:44.200][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:03:44.200][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:03:44.201][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:03:44.202][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.203][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.204][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:03:44.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.206][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.207][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.208][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:03:44.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:03:44.210][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.210][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.212][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-06 16:03:44.213][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.214][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:03:44.215][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.216][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:03:44.217][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.218][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.218][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.219][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.220][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:03:44.221][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:03:44.222][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.223][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-06 16:03:44.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:03:44.225][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.226][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.226][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:03:44.226][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-06 16:03:44.226][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-06 16:03:44.226][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-06 16:03:44.226][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-06 16:03:44.227][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:03:44.228][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.229][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.230][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:03:44.231][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.232][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.233][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.234][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:03:44.235][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:03:44.236][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.237][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.238][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-06 16:03:44.239][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.240][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-06 16:03:44.241][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.242][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:03:44.243][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.244][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.245][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.246][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-06 16:03:44.247][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:03:44.248][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.249][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-06 16:03:44.250][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:03:44.251][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.252][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.253][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.253][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:03:44.254][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.255][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.256][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:03:44.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.258][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.259][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.260][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:03:44.261][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:03:44.262][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.263][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.264][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-06 16:03:44.265][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.266][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-06 16:03:44.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:03:44.269][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.270][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.271][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.272][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.272][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-06 16:03:44.273][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:03:44.274][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.275][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-06 16:03:44.276][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:03:44.277][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.278][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.279][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.280][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-06 16:03:44.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.282][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:03:44.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.284][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.285][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.285][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:03:44.287][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:03:44.288][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.289][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.293][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:03:44.294][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.294][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.298][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.302][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.306][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.310][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.322][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.326][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.330][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.337][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.341][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.345][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.354][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.358][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.363][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.367][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.371][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.373][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-06 16:03:44.378][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-06 16:03:44.380][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-06 16:03:44.381][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-06 16:03:44.383][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-06 16:03:44.384][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:03:44.385][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-06 16:03:44.387][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-06 16:03:44.388][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-06 16:03:44.389][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:03:44.391][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:03:44.392][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-06 16:03:44.394][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-06 16:03:44.395][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-06 16:03:44.396][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-06 16:03:44.398][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:03:44.399][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-06 16:03:44.400][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-06 16:03:44.402][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-06 16:03:44.403][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-06 16:03:44.405][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-06 16:03:44.406][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-06 16:03:44.407][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-06 16:03:44.409][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-06 16:03:44.410][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-06 16:03:44.412][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-06 16:03:44.413][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-06 16:03:44.414][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-06 16:03:44.416][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-06 16:03:44.417][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-06 16:03:44.418][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-06 16:03:44.420][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-06 16:03:44.421][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-06 16:03:44.423][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-06 16:03:44.424][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-06 16:03:44.425][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-06 16:03:44.427][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-06 16:03:44.428][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-06 16:03:44.429][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-06 16:03:44.431][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-06 16:03:44.432][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-06 16:03:44.433][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-06 16:03:44.435][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-06 16:03:44.436][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-06 16:03:44.438][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-06 16:03:44.439][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-06 16:03:44.440][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-06 16:03:44.442][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-06 16:03:44.443][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-06 16:03:44.445][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-06 16:03:44.446][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-06 16:03:44.447][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-06 16:03:44.449][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-06 16:03:44.450][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-06 16:03:44.451][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-06 16:03:44.453][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-06 16:03:44.454][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-06 16:03:44.456][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-06 16:03:44.457][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-06 16:03:44.458][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-06 16:03:44.460][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-06 16:03:44.461][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-06 16:03:44.462][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-06 16:03:44.464][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-06 16:03:44.465][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-06 16:03:44.467][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-06 16:03:44.468][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-06 16:03:44.469][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-06 16:03:44.471][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-06 16:03:44.472][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-06 16:03:44.473][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-06 16:03:44.475][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-06 16:03:44.476][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-06 16:03:44.477][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-06 16:03:44.479][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-06 16:03:44.480][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-06 16:03:44.481][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-06 16:03:44.483][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-06 16:03:44.484][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-06 16:03:44.485][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-06 16:03:44.487][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-06 16:03:44.488][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-06 16:03:44.489][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-06 16:03:44.507][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-06 16:03:44.509][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-06 16:03:44.512][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-06 16:03:44.513][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.515][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.516][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[2024-07-06 16:03:44.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.526][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.532][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.538][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.543][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.560][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.565][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.576][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.581][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.592][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.598][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.609][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.615][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-06 16:03:44.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-06 16:03:44.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-06 16:03:44.622][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-07-06 16:03:44.631][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-07-06 16:03:44.632][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.633][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.634][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.635][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-06 16:03:44.636][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.637][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-07-06 16:03:44.638][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.639][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-06 16:03:44.640][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-06 16:03:44.641][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.642][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-07-06 16:03:44.643][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-07-06 16:03:44.644][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-07-06 16:03:44.645][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-06 16:03:44.646][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-06 16:03:44.646][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-07-06 16:03:44.646][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-07-06 16:03:44.647][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-06 16:03:44.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.648][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.649][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-06 16:03:44.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-06 16:03:44.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-06 16:03:44.652][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-06 16:03:44.653][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-07-06 16:03:44.653][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-07-06 16:03:44.654][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-06 16:03:44.654][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-06 16:03:44.655][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-06 16:03:44.656][self$setPropertyValue]
biodb.DEBUG[2024-07-06 16:03:44.665][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-07-06 16:03:44.667][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-06 16:03:44.668][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-06 16:03:44.669][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-06 16:03:44.671][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-06 16:03:44.693][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-07-06 16:03:44.694][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-07-06 16:03:44.698][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-07-06 16:03:44.702][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-07-06 16:03:44.707][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:03:44.708][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-06 16:03:44.709][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-07-06 16:03:44.710][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-07-06 16:03:44.719][biodb::testThat]
biodb.INFO [2024-07-06 16:03:44.720][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-06 16:03:44.721][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:03:44.722][biodb::testThat]
biodb.TRACE[2024-07-06 16:03:44.725][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-07-06 16:03:44.727][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:03:44.731][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-07-06 16:03:44.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:03:44.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:44.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:44.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:44.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:44.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:44.754][FUN] Functions in observer BiodbConfig: [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[2024-07-06 16:03:44.766][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:44.767][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:44.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.769][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:44.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:44.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.785][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:44.786][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:44.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.787][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.811][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:44.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:44.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.815][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:44.816][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:44.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.818][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.819][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:44.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:44.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.822][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:44.823][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:44.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.825][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.826][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:44.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:44.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.830][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:44.831][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:44.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.833][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:44.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:44.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.837][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:44.838][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:44.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.840][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:44.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:44.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.882][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:44.882][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:44.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.884][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.885][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:44.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:44.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.889][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:44.890][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:44.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.891][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.893][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:44.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:44.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.896][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:44.897][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:44.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.899][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:44.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:44.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.904][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:44.905][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:44.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.906][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:44.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:44.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.911][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:44.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:44.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.914][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.915][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:44.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:44.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.918][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:44.919][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:44.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.921][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:44.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:44.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.926][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:44.926][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:44.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.928][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:44.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:44.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.933][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:44.934][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:44.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.935][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:44.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:44.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.940][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:44.941][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:44.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.943][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.944][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:44.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:44.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.947][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:44.948][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:44.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.950][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.951][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:44.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:44.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.955][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:44.955][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:44.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.957][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.958][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:44.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.962][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-07-06 16:03:44.963][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:44.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.965][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.966][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-07-06 16:03:44.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:44.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:44.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:44.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:44.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:44.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:44.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:44.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:44.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:44.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.013][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.017][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.020][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.024][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.027][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.031][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.055][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.059][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.062][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.069][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.073][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.087][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.090][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.094][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.101][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.104][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.108][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.115][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.118][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.128][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.136][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.139][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.157][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.164][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.167][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.171][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.174][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.178][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.181][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.185][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.188][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.192][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.195][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-07-06 16:03:45.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.202][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.209][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-07-06 16:03:45.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.242][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.246][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.250][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.256][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:45.285][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-07-06 16:03:45.287][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:03:45.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:03:45.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.291][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:03:45.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:03:45.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:03:45.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:03:45.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:03:45.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:03:45.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.329][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.359][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.362][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.366][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:45.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.385][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.386][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.388][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.404][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.407][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.411][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.414][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.415][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.417][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.418][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.438][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.439][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.441][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.451][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.455][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.458][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.462][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.463][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.464][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.465][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.486][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.488][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.498][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.502][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.506][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.509][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.510][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.512][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.513][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.536][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.537][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.539][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.540][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.550][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.553][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.557][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.560][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.561][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.563][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.564][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.573][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.577][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.581][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.584][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.585][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.587][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.597][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.601][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.604][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.608][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.609][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.610][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.611][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.631][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.632][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.633][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.634][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.644][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.648][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.655][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.659][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.660][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.661][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.662][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.675][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.679][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.682][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.683][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.685][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.686][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.699][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.706][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.707][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.709][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.719][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.723][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.730][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.732][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.733][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.754][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.755][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.756][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.782][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.783][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.784][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.795][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.798][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.802][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.805][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.806][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.808][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.809][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.818][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:45.819][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:45.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.821][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.825][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.826][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:45.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.827][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.831][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.832][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:45.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.834][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.838][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:45.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.840][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.844][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.844][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:45.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.846][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.850][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.851][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:45.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.852][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.856][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.857][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:45.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.859][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.862][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.863][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:45.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.865][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.869][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:45.869][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:45.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.871][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.875][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:45.876][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:45.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.877][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.881][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:45.882][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:45.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.883][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.887][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.888][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:45.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.890][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.893][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.894][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:45.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.896][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.899][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.900][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:45.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.902][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.909][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:45.910][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:45.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.912][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.915][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.916][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:45.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.918][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.922][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.923][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:45.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.924][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:45.928][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:45.929][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:45.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:45.930][ef$get] fields variable is a list.
biodb.INFO [2024-07-06 16:03:45.936][biodb::testThat]
biodb.INFO [2024-07-06 16:03:45.937][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-06 16:03:45.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:03:45.939][biodb::testThat]
biodb.DEBUG[2024-07-06 16:03:45.951][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-06 16:03:45.958][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-07-06 16:03:45.963][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:45.964][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-07-06 16:03:45.966][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-07-06 16:03:45.967][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-06 16:03:45.969][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-07-06 16:03:45.970][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-07-06 16:03:45.992][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-07-06 16:03:45.993][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-07-06 16:03:45.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-06 16:03:45.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:03:45.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:03:46.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:03:46.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:03:46.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:03:46.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-06 16:03:46.005][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.008][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.013][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.014][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.015][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.016][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.020][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.021][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.023][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.024][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.027][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.028][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.030][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.036][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.039][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.040][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.042][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.047][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.048][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.049][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.054][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.055][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.057][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.058][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.061][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.062][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.064][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.065][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.069][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.070][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.071][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.072][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.076][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.077][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.079][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.083][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:46.084][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:46.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.086][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.087][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:46.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:46.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.091][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:46.092][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:46.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.093][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:46.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:46.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.100][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.105][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.106][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.108][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.112][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.113][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.115][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.116][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.120][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.121][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.122][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.123][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.127][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:46.128][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:46.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.130][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.131][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:46.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:46.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.134][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-07-06 16:03:46.135][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:46.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.137][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.138][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-07-06 16:03:46.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:46.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.152][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.156][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.163][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-06 16:03:46.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.167][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.170][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.173][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-06 16:03:46.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-06 16:03:46.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-06 16:03:46.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.198][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-06 16:03:46.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.209][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.212][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.216][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-06 16:03:46.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.219][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:46.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:46.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.223][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:46.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:46.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:46.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-06 16:03:46.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.230][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.233][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.237][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:46.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:46.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:46.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:46.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-06 16:03:46.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-06 16:03:46.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:46.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:46.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:46.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:46.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-06 16:03:46.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-06 16:03:46.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.272][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.276][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.279][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-06 16:03:46.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-06 16:03:46.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.307][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.311][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-06 16:03:46.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.318][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.321][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.325][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.328][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:46.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:46.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.332][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:46.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:46.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.335][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-06 16:03:46.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-06 16:03:46.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.339][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-07-06 16:03:46.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.353][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-07-06 16:03:46.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-06 16:03:46.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.375][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:46.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:46.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.379][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:46.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:46.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.386][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:46.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-06 16:03:46.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-06 16:03:46.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-06 16:03:46.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.414][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-07-06 16:03:46.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-06 16:03:46.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-06 16:03:46.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:03:46.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-06 16:03:46.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:03:46.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-06 16:03:46.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:03:46.432][biodb::testThat]
biodb.INFO [2024-07-06 16:03:46.433][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-06 16:03:46.434][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:03:46.435][biodb::testThat]
biodb.TRACE[2024-07-06 16:03:46.437][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.438][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.440][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.441][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-07-06 16:03:46.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.476][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-07-06 16:03:46.477][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-07-06 16:03:46.478][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-07-06 16:03:46.479][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-07-06 16:03:46.480][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.481][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.483][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-07-06 16:03:46.484][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.485][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-07-06 16:03:46.486][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-07-06 16:03:46.487][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-07-06 16:03:46.488][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-07-06 16:03:46.489][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-07-06 16:03:46.490][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-07-06 16:03:46.491][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-07-06 16:03:46.492][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.506][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-07-06 16:03:46.507][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-07-06 16:03:46.508][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-07-06 16:03:46.517][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.518][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.520][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.521][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-07-06 16:03:46.530][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.538][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.541][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.547][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2024-07-06 16:03:46.595][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-07-06 16:03:46.596][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-07-06 16:03:46.597][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-07-06 16:03:46.609][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.611][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.612][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-07-06 16:03:46.613][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.614][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-07-06 16:03:46.628][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-07-06 16:03:46.629][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-07-06 16:03:46.630][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-07-06 16:03:46.631][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-07-06 16:03:46.632][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-07-06 16:03:46.632][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-07-06 16:03:46.634][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.642][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.645][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.649][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:03:46.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:03:46.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.652][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-07-06 16:03:46.653][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-07-06 16:03:46.654][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-07-06 16:03:46.664][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.665][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.666][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.667][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-07-06 16:03:46.676][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.680][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.684][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.689][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-07-06 16:03:46.690][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-07-06 16:03:46.691][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-07-06 16:03:46.692][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-07-06 16:03:46.693][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.695][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.696][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-07-06 16:03:46.697][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.698][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-07-06 16:03:46.699][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-07-06 16:03:46.700][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-07-06 16:03:46.701][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-07-06 16:03:46.702][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-07-06 16:03:46.703][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-07-06 16:03:46.703][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-07-06 16:03:46.705][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.709][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.712][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.716][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:03:46.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.719][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-07-06 16:03:46.720][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-07-06 16:03:46.721][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-07-06 16:03:46.732][biodb::testThat]
biodb.INFO [2024-07-06 16:03:46.733][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-06 16:03:46.734][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:03:46.735][biodb::testThat]
biodb.TRACE[2024-07-06 16:03:46.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.767][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-07-06 16:03:46.768][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-07-06 16:03:46.769][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-07-06 16:03:46.770][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.771][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.773][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-07-06 16:03:46.774][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-07-06 16:03:46.775][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-07-06 16:03:46.776][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-07-06 16:03:46.777][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-07-06 16:03:46.778][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-07-06 16:03:46.779][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-07-06 16:03:46.779][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-07-06 16:03:46.780][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-07-06 16:03:46.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:03:46.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:03:46.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-06 16:03:46.796][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-07-06 16:03:46.797][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-07-06 16:03:46.809][biodb::testThat]
biodb.INFO [2024-07-06 16:03:46.810][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-06 16:03:46.810][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:03:46.811][biodb::testThat]
biodb.TRACE[2024-07-06 16:03:46.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:03:46.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:03:46.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.832][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:03:46.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:03:46.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.836][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:03:46.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:03:46.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.839][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:03:46.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:03:46.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.883][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:03:46.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:03:46.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.887][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-06 16:03:46.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-06 16:03:46.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.890][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-06 16:03:46.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-06 16:03:46.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:03:46.894][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-06 16:03:46.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-06 16:03:46.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:03:46.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-06 16:03:46.902][biodb::testThat]
biodb.INFO [2024-07-06 16:03:46.903][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-06 16:03:46.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:03:46.905][biodb::testThat]
biodb.INFO [2024-07-06 16:03:46.911][biodb::testThat]
biodb.INFO [2024-07-06 16:03:46.912][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-06 16:03:46.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:03:46.914][biodb::testThat]
biodb.INFO [2024-07-06 16:03:46.920][biodb::testThat]
biodb.INFO [2024-07-06 16:03:46.921][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-06 16:03:46.922][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:03:46.922][biodb::testThat]
biodb.DEBUG[2024-07-06 16:03:46.925][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-07-06 16:04:02.844][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-07-06 16:04:02.882][biodb::testThat]
biodb.INFO [2024-07-06 16:04:02.884][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-06 16:04:02.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-06 16:04:02.888][biodb::testThat]
biodb.DEBUG[2024-07-06 16:04:08.758][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-07-06 16:04:08.783][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:08.786][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:08.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:08.790][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:08.792][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:04:08.794][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:04:08.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:08.799][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:08.801][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:04:08.803][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:04:08.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:08.807][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:08.809][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-06 16:04:08.812][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-06 16:04:08.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:08.815][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:08.817][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-06 16:04:08.819][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-06 16:04:08.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:08.822][ef$get] fields variable is a list.
biodb.TRACE[2024-07-06 16:04:08.824][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-06 16:04:08.826][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-06 16:04:08.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-06 16:04:08.829][ef$get] fields variable is a list.
biodb.INFO [2024-07-06 16:04:08.830][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-06 16:04:08.832][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-07-06 16:04:08.833][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-07-06 16:04:08.835][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-06 16:04:08.836][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-06 16:04:08.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-06 16:04:08.838][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-06 16:04:08.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-06 16:04:08.841][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-06 16:04:08.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 147 ]
> 
> proc.time()
   user  system elapsed 
  4.777   0.244  26.545

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 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 ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
* 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 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’
 OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)