Back to Long Tests report for BioC 3.20

This page was generated on 2024-11-02 23:55 -0400 (Sat, 02 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4505
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
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 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-11-02 09:55 -0400 (Sat, 02 Nov 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_20
git_last_commit: 0eb718c
git_last_commit_date: 2024-10-29 11:06:39 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-11-02 16:08:04 -0400 (Sat, 02 Nov 2024)
EndedAt: 2024-11-02 16:13:09 -0400 (Sat, 02 Nov 2024)
EllapsedTime: 305.2 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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # 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 [2024-11-02 16:12:48.482][biodb::testContext]
biodb.INFO [2024-11-02 16:12:48.483][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 16:12:48.484][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-11-02 16:12:48.485][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 16:12:48.486][biodb::testContext]
biodb.INFO [2024-11-02 16:12:48.491][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-02 16:12:48.493][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-02 16:12:48.499][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:12:48.500][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-02 16:12:48.501][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-02 16:12:48.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.504][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-02 16:12:48.520][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-02 16:12:48.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.523][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.524][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-02 16:12:48.524][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-02 16:12:48.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.528][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-02 16:12:48.529][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-02 16:12:48.529][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-02 16:12:48.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.532][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[2024-11-02 16:12:48.533][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-02 16:12:48.534][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-02 16:12:48.534][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-02 16:12:48.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.538][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-02 16:12:48.539][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-02 16:12:48.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.541][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.542][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-02 16:12:48.543][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-02 16:12:48.544][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-02 16:12:48.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.547][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-02 16:12:48.548][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-02 16:12:48.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.551][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-02 16:12:48.552][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-02 16:12:48.553][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-02 16:12:48.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.556][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-02 16:12:48.557][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-02 16:12:48.558][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-02 16:12:48.558][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-02 16:12:48.559][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-02 16:12:48.560][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-02 16:12:48.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.563][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-02 16:12:48.564][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-02 16:12:48.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.567][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-02 16:12:48.568][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-02 16:12:48.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.572][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-02 16:12:48.572][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-02 16:12:48.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.576][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-02 16:12:48.577][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 16:12:48.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.580][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-02 16:12:48.581][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-02 16:12:48.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.584][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-02 16:12:48.585][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-02 16:12:48.589][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-02 16:12:48.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.592][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-02 16:12:48.593][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-02 16:12:48.594][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-02 16:12:48.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.599][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-02 16:12:48.633][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.647][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-02 16:12:48.648][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:12:48.649][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.650][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.651][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.653][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 16:12:48.654][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:12:48.655][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.655][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-02 16:12:48.656][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:12:48.657][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.658][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.659][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:12:48.659][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 16:12:48.659][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 16:12:48.659][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 16:12:48.659][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 16:12:48.660][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:12:48.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:48.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:48.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:12:48.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:48.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:48.665][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.666][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:12:48.667][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:12:48.668][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.669][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.670][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-02 16:12:48.672][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.672][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 16:12:48.673][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.674][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:12:48.675][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.676][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.677][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.678][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.679][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 16:12:48.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:12:48.680][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.681][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-02 16:12:48.682][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:12:48.683][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.684][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.685][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:12:48.685][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 16:12:48.685][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 16:12:48.685][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 16:12:48.685][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 16:12:48.686][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:12:48.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:48.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:48.688][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:12:48.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:48.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:48.691][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.691][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:12:48.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:12:48.694][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.695][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.696][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-02 16:12:48.697][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.698][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-02 16:12:48.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:12:48.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.703][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.703][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.704][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 16:12:48.705][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:12:48.706][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.707][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-02 16:12:48.708][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:12:48.709][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.709][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.710][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.711][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:12:48.712][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:48.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:48.714][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:12:48.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:48.715][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:48.716][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.717][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.718][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:12:48.719][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:12:48.719][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.720][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.721][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-02 16:12:48.723][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.724][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 16:12:48.725][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:12:48.726][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.727][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.728][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.729][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.730][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 16:12:48.731][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:12:48.732][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.733][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-02 16:12:48.733][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:12:48.734][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.735][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:48.736][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.737][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:12:48.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:48.738][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:48.739][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:12:48.740][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:48.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:48.742][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:12:48.743][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.743][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:12:48.744][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:12:48.745][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:48.746][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:48.749][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:12:48.750][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.751][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.758][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.762][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.766][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.770][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.777][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.781][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.785][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.789][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.796][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.800][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.808][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:48.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.816][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.820][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.821][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-02 16:12:48.825][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-02 16:12:48.826][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-02 16:12:48.827][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-02 16:12:48.828][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 16:12:48.829][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 16:12:48.831][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-02 16:12:48.832][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-02 16:12:48.833][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-02 16:12:48.834][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 16:12:48.836][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 16:12:48.837][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-02 16:12:48.838][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-02 16:12:48.839][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-02 16:12:48.840][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-02 16:12:48.842][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 16:12:48.843][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-02 16:12:48.844][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-02 16:12:48.845][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 16:12:48.847][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-02 16:12:48.848][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-02 16:12:48.849][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-02 16:12:48.850][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-02 16:12:48.852][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-02 16:12:48.853][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-02 16:12:48.854][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-02 16:12:48.855][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-02 16:12:48.856][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-02 16:12:48.858][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-02 16:12:48.859][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-02 16:12:48.860][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-02 16:12:48.861][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-02 16:12:48.863][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-02 16:12:48.864][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-02 16:12:48.865][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-02 16:12:48.866][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-02 16:12:48.867][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-02 16:12:48.869][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-02 16:12:48.870][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-02 16:12:48.871][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-02 16:12:48.872][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-02 16:12:48.874][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-02 16:12:48.875][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-02 16:12:48.876][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-02 16:12:48.877][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-02 16:12:48.879][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-02 16:12:48.880][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-02 16:12:48.881][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-02 16:12:48.882][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-02 16:12:48.883][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-02 16:12:48.885][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-02 16:12:48.886][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-02 16:12:48.887][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-02 16:12:48.888][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-02 16:12:48.890][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-02 16:12:48.891][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-02 16:12:48.892][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-02 16:12:48.893][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-02 16:12:48.895][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-02 16:12:48.896][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-02 16:12:48.897][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-02 16:12:48.898][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-02 16:12:48.899][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-02 16:12:48.901][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-02 16:12:48.902][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-02 16:12:48.903][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-02 16:12:48.904][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 16:12:48.906][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 16:12:48.907][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-02 16:12:48.908][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-02 16:12:48.909][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-02 16:12:48.910][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-02 16:12:48.912][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-02 16:12:48.913][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-02 16:12:48.914][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-02 16:12:48.915][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-02 16:12:48.916][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-02 16:12:48.918][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-02 16:12:48.919][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-02 16:12:48.920][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-02 16:12:48.921][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-02 16:12:48.922][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-02 16:12:48.924][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-02 16:12:48.932][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-02 16:12:48.934][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-02 16:12:48.936][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:12:48.937][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.939][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.939][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.948][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.954][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.959][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.964][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.970][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.975][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.981][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.986][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:48.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:48.992][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:48.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:48.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:48.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:48.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:48.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.004][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:49.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.011][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:49.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.017][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:49.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.023][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:49.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.029][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:49.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.035][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:49.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.042][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:49.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.048][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.049][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 16:12:49.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:12:49.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:12:49.057][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-11-02 16:12:49.067][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:12:49.070][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:49.071][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-02 16:12:49.072][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:49.072][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:12:49.073][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:49.074][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-11-02 16:12:49.075][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:49.076][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:12:49.077][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-02 16:12:49.078][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:12:49.079][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:49.080][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-11-02 16:12:49.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-11-02 16:12:49.082][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-11-02 16:12:49.083][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-02 16:12:49.084][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:12:49.084][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-11-02 16:12:49.084][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-11-02 16:12:49.085][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-02 16:12:49.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:49.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:49.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:12:49.089][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:12:49.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:12:49.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:12:49.092][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-02 16:12:49.092][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-11-02 16:12:49.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:12:49.094][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:12:49.094][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-02 16:12:49.095][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:12:49.113][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-11-02 16:12:49.114][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 16:12:49.115][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 16:12:49.117][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 16:12:49.119][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 16:12:49.140][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:12:49.141][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-11-02 16:12:49.145][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:12:49.149][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-02 16:12:49.153][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 16:12:49.154][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 16:12:49.155][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-11-02 16:12:49.156][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-11-02 16:12:49.164][biodb::testThat]
biodb.INFO [2024-11-02 16:12:49.165][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-11-02 16:12:49.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:12:49.167][biodb::testThat]
biodb.TRACE[2024-11-02 16:12:49.170][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[2024-11-02 16:12:49.172][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-02 16:12:49.175][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-02 16:12:49.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 16:12:49.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:49.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:49.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:49.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:49.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:49.197][FUN] Functions in observer BiodbConfig: [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[2024-11-02 16:12:49.207][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.208][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.210][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.226][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.227][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.229][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.252][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.256][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.257][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.258][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.259][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.263][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.264][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.266][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.267][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.270][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.271][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.273][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.278][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.279][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.280][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.319][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.320][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.321][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.322][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.326][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.327][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.329][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.330][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.333][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.334][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.336][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.337][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.341][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.342][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.343][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.344][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.348][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:49.349][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:49.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.351][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.352][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:49.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:49.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.355][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:49.356][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:49.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.358][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.362][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.363][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.365][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.370][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.371][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.371][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.372][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.377][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.378][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.380][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.384][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.385][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.387][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.388][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.391][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:49.392][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:49.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.394][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.395][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:49.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:49.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.399][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:12:49.400][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:49.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.401][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.402][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:12:49.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:49.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.449][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.452][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.455][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:49.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.459][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.463][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.466][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:49.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.494][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.497][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:49.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.501][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.504][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:49.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.511][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:49.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:49.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.515][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:49.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:49.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:49.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:49.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.522][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.525][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.529][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.532][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:49.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:49.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:49.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:49.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:49.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:49.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:49.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:49.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:49.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:49.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:49.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:49.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.560][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.563][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.567][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.573][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:49.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.597][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.604][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.608][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.611][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.614][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.618][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:49.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:49.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:49.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:49.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.625][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:49.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:49.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.628][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:12:49.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.642][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:12:49.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:49.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.664][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.682][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.688][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:49.715][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-02 16:12:49.718][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:12:49.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:12:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.721][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:12:49.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:12:49.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:12:49.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:12:49.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.728][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:12:49.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:12:49.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.786][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.790][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.793][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:49.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.812][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.813][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.815][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:49.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:49.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.829][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.832][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.836][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.839][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.840][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.842][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.843][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:49.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.863][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.863][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.865][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:49.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.875][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.879][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.882][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.886][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.887][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.888][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.889][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:49.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.909][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.910][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.911][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:49.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.922][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.925][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.929][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.932][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.933][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.935][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.935][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:49.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.958][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.959][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.960][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:49.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:49.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.971][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.974][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.978][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.981][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.982][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.984][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.984][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:49.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:49.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.994][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:49.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:49.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:49.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:49.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:49.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:49.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.001][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.004][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.005][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.007][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.007][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.017][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.020][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.024][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.027][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.028][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.030][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.031][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.050][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.051][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.053][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.070][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.076][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.077][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.079][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.096][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.099][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.100][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.102][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.103][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.116][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.122][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.123][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.125][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.135][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.139][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.142][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.145][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.146][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.148][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.149][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.169][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.169][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.171][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.172][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.192][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.193][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.194][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.198][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.207][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.210][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.214][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.217][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.218][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.220][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.221][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.230][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.231][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.233][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.236][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.237][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.239][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.242][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.243][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.245][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.249][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.251][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.255][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.255][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.257][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.261][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.262][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.263][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.267][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.268][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.269][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.273][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.274][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.275][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.279][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.280][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.281][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.285][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.286][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.288][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.291][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.292][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.294][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.297][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.298][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.299][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.300][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.303][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.304][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.306][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.309][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.310][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.312][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.316][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.316][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.321][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.325][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.325][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.327][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.331][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.332][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.333][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.337][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.338][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.339][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 16:12:50.345][biodb::testThat]
biodb.INFO [2024-11-02 16:12:50.346][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-02 16:12:50.347][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:12:50.348][biodb::testThat]
biodb.DEBUG[2024-11-02 16:12:50.360][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-11-02 16:12:50.366][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-02 16:12:50.370][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:50.371][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-11-02 16:12:50.372][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-11-02 16:12:50.374][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 16:12:50.376][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-11-02 16:12:50.377][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 16:12:50.398][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-02 16:12:50.399][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-02 16:12:50.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 16:12:50.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:12:50.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:12:50.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:12:50.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:12:50.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:12:50.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 16:12:50.411][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.412][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.413][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.418][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.419][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.420][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.422][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.425][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.426][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.428][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.429][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.432][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.433][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.435][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.436][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.440][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.444][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.446][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.450][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.451][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.453][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.458][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.458][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.460][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.461][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.465][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.466][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.467][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.468][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.472][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.473][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.475][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.479][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.480][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.482][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.486][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.487][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.489][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.494][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.494][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.496][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.501][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.502][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.503][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.508][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.509][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.510][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.515][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.516][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.518][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.522][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.523][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.525][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.526][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.529][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.530][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.532][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.533][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.536][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:12:50.537][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.539][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.540][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:12:50.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.554][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.558][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.561][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:12:50.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.567][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.571][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.574][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:12:50.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:12:50.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:12:50.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.598][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.602][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:12:50.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.609][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:12:50.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.619][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.623][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.626][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:12:50.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.630][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.633][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.637][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.640][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.643][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.647][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:12:50.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:12:50.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:12:50.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:12:50.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.671][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.675][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.678][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:12:50.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:12:50.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.705][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.709][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.712][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:12:50.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.719][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.723][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:50.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.733][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:12:50.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:12:50.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.737][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:12:50.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.751][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:12:50.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:12:50.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.773][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:50.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:50.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.776][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:50.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:50.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.783][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:50.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:12:50.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:12:50.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:12:50.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:50.808][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-02 16:12:50.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-02 16:12:50.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-02 16:12:50.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-02 16:12:50.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-02 16:12:50.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-02 16:12:50.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-02 16:12:50.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 16:12:50.829][biodb::testThat]
biodb.INFO [2024-11-02 16:12:50.829][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-02 16:12:50.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:12:50.831][biodb::testThat]
biodb.TRACE[2024-11-02 16:12:50.834][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.835][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.836][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:50.837][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-11-02 16:12:50.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:50.871][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-11-02 16:12:50.873][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-11-02 16:12:50.873][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:12:50.874][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:12:50.876][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:50.877][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:50.878][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:12:50.880][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:50.880][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:12:50.882][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:12:50.882][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:12:50.883][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-02 16:12:50.884][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-02 16:12:50.885][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-02 16:12:50.886][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-02 16:12:50.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.895][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:50.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:50.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:50.902][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:12:50.903][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-02 16:12:50.903][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-11-02 16:12:50.912][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.913][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.915][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:50.916][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-11-02 16:12:50.925][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.928][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:50.936][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:50.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:50.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:50.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:50.941][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[2024-11-02 16:12:50.988][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-11-02 16:12:50.989][private$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[2024-11-02 16:12:50.990][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-11-02 16:12:51.002][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.004][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.005][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:12:51.006][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.007][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:12:51.021][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:12:51.021][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:12:51.022][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-02 16:12:51.023][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-02 16:12:51.024][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-02 16:12:51.025][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-02 16:12:51.026][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:51.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:51.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.030][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:51.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:51.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.034][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:51.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:51.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.040][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:12:51.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:12:51.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:51.044][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:12:51.045][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-02 16:12:51.045][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-11-02 16:12:51.054][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.055][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.057][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:51.058][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-11-02 16:12:51.067][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.071][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.074][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:51.080][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-11-02 16:12:51.081][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-11-02 16:12:51.082][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-11-02 16:12:51.083][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-11-02 16:12:51.084][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.085][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.087][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:12:51.088][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.089][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:12:51.090][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:12:51.091][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:12:51.092][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-02 16:12:51.092][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-02 16:12:51.093][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-02 16:12:51.094][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-02 16:12:51.096][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.099][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.103][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.106][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:12:51.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:51.110][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:12:51.111][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-02 16:12:51.111][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-11-02 16:12:51.123][biodb::testThat]
biodb.INFO [2024-11-02 16:12:51.124][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-11-02 16:12:51.124][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:12:51.125][biodb::testThat]
biodb.TRACE[2024-11-02 16:12:51.134][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:51.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:51.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:51.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:51.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:51.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:51.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:51.152][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-11-02 16:12:51.153][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:12:51.154][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:12:51.156][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.157][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.162][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:12:51.163][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:12:51.164][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:12:51.165][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:12:51.166][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:12:51.167][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-02 16:12:51.168][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-02 16:12:51.168][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-02 16:12:51.169][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-02 16:12:51.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:51.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:51.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:51.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.178][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:51.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:51.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.181][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:12:51.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:12:51.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:12:51.185][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:12:51.186][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-11-02 16:12:51.197][biodb::testThat]
biodb.INFO [2024-11-02 16:12:51.198][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-11-02 16:12:51.199][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:12:51.199][biodb::testThat]
biodb.TRACE[2024-11-02 16:12:51.217][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:12:51.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:12:51.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.220][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:12:51.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:12:51.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.224][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:12:51.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:12:51.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.227][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:12:51.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:12:51.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:12:51.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:12:51.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.274][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:12:51.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:12:51.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.277][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:12:51.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:12:51.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:12:51.281][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:12:51.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:12:51.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:12:51.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 16:12:51.288][biodb::testThat]
biodb.INFO [2024-11-02 16:12:51.289][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-02 16:12:51.290][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:12:51.291][biodb::testThat]
biodb.INFO [2024-11-02 16:12:51.297][biodb::testThat]
biodb.INFO [2024-11-02 16:12:51.298][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-02 16:12:51.299][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:12:51.300][biodb::testThat]
biodb.INFO [2024-11-02 16:12:51.306][biodb::testThat]
biodb.INFO [2024-11-02 16:12:51.306][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-02 16:12:51.307][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:12:51.308][biodb::testThat]
biodb.DEBUG[2024-11-02 16:12:51.311][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-11-02 16:13:07.521][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-11-02 16:13:07.571][biodb::testThat]
biodb.INFO [2024-11-02 16:13:07.573][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-02 16:13:07.575][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:13:07.577][biodb::testThat]
biodb.DEBUG[2024-11-02 16:13:08.250][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-11-02 16:13:08.325][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:13:08.327][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:13:08.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:13:08.332][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:13:08.334][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:13:08.336][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:13:08.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:13:08.340][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:13:08.342][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:13:08.345][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:13:08.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:13:08.349][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:13:08.351][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:13:08.353][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:13:08.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:13:08.357][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:13:08.359][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:13:08.361][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:13:08.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:13:08.365][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:13:08.367][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:13:08.368][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:13:08.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:13:08.371][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 16:13:08.373][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-02 16:13:08.375][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-11-02 16:13:08.376][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-11-02 16:13:08.378][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-02 16:13:08.379][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:13:08.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:13:08.381][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:13:08.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:13:08.384][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:13:08.385][FUN] Functions in observer 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 
  4.540   0.202  21.433

'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_1.12.0.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 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 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 ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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 13.2.0-23ubuntu4) 13.2.0’
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)