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 lconway

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: /Library/Frameworks/R.framework/Resources/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 16:01:07 -0400 (Sat, 02 Nov 2024)
EndedAt: 2024-11-02 16:06:13 -0400 (Sat, 02 Nov 2024)
EllapsedTime: 305.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 1

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-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-11-02 16:05:48.469][biodb::testContext]
biodb.INFO [2024-11-02 16:05:48.472][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 16:05:48.473][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-11-02 16:05:48.474][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-02 16:05:48.474][biodb::testContext]
biodb.INFO [2024-11-02 16:05:48.479][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-02 16:05:48.481][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-11-02 16:05:48.486][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:05:48.487][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-02 16:05:48.488][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-02 16:05:48.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.491][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-02 16:05:48.504][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-02 16:05:48.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.506][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.507][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-02 16:05:48.507][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-02 16:05:48.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.510][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-02 16:05:48.511][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-02 16:05:48.512][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-02 16:05:48.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.514][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.514][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-02 16:05:48.515][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-02 16:05:48.516][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-02 16:05:48.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.518][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-02 16:05:48.519][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-02 16:05:48.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.521][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.522][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-02 16:05:48.522][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-02 16:05:48.523][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-02 16:05:48.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.526][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-02 16:05:48.527][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-02 16:05:48.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.529][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.530][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-02 16:05:48.531][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-02 16:05:48.532][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-02 16:05:48.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.534][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-02 16:05:48.535][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-02 16:05:48.536][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-02 16:05:48.537][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-02 16:05:48.537][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-02 16:05:48.538][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-02 16:05:48.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.540][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.541][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-02 16:05:48.542][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-02 16:05:48.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.544][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-02 16:05:48.545][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-02 16:05:48.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.547][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.548][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-02 16:05:48.549][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-02 16:05:48.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.552][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-02 16:05:48.553][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 16:05:48.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.555][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 16:05:48.555][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-02 16:05:48.556][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-02 16:05:48.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.559][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-02 16:05:48.559][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-02 16:05:48.576][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-11-02 16:05:48.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.579][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-02 16:05:48.580][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-02 16:05:48.581][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-02 16:05:48.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.585][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-02 16:05:48.610][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.626][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-02 16:05:48.627][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.628][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:05:48.628][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.629][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.630][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.631][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.631][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 16:05:48.632][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:05:48.633][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.634][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-02 16:05:48.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:05:48.635][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.636][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.637][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:05:48.637][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 16:05:48.637][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 16:05:48.637][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 16:05:48.637][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 16:05:48.637][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:05:48.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.639][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:05:48.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.641][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.642][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.643][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:05:48.643][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:05:48.644][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.645][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.645][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-02 16:05:48.647][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.647][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 16:05:48.648][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.649][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:05:48.650][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.651][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.651][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.653][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 16:05:48.654][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:05:48.654][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.655][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-02 16:05:48.656][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:05:48.657][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.657][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.658][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:05:48.658][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-02 16:05:48.658][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-02 16:05:48.658][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-02 16:05:48.658][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-02 16:05:48.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:05:48.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.660][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.661][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:05:48.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.663][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.664][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.664][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:05:48.665][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:05:48.666][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.666][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.668][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-02 16:05:48.669][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.670][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-02 16:05:48.671][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.671][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:05:48.672][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.673][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.673][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.674][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.675][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-02 16:05:48.676][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:05:48.676][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.677][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-02 16:05:48.678][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:05:48.679][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.679][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.680][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.681][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:05:48.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.683][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:05:48.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.685][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.686][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.687][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:05:48.687][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:05:48.688][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.689][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.690][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-02 16:05:48.691][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.692][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-02 16:05:48.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:05:48.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.696][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.696][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.697][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-02 16:05:48.698][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:05:48.698][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.699][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-02 16:05:48.700][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:05:48.701][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.701][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.702][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.703][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-02 16:05:48.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.705][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:05:48.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.707][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.708][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.709][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:05:48.710][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:05:48.711][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.712][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.714][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:05:48.715][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.716][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:05:48.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.721][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 16:05:48.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.723][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.725][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 16:05:48.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.726][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.728][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 16:05:48.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.729][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.731][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 16:05:48.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.733][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.735][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 16:05:48.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.736][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.738][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 16:05:48.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.739][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.741][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 16:05:48.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.743][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:05:48.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.746][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.748][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 16:05:48.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.755][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 16:05:48.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.757][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.759][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 16:05:48.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.760][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.762][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 16:05:48.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.763][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.765][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 16:05:48.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.768][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 16:05:48.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.770][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 16:05:48.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.772][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 16:05:48.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.775][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 16:05:48.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.776][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.777][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-02 16:05:48.780][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-02 16:05:48.781][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-02 16:05:48.782][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-02 16:05:48.783][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-02 16:05:48.784][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 16:05:48.785][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-02 16:05:48.786][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-02 16:05:48.787][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-02 16:05:48.788][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 16:05:48.789][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 16:05:48.790][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-02 16:05:48.791][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-02 16:05:48.793][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-02 16:05:48.794][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-02 16:05:48.794][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 16:05:48.796][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-02 16:05:48.797][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-02 16:05:48.798][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-02 16:05:48.799][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-02 16:05:48.800][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-02 16:05:48.801][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-02 16:05:48.802][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-02 16:05:48.803][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-02 16:05:48.804][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-02 16:05:48.805][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-02 16:05:48.806][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-02 16:05:48.807][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-02 16:05:48.808][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-02 16:05:48.809][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-02 16:05:48.810][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-02 16:05:48.811][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-02 16:05:48.812][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-02 16:05:48.813][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-02 16:05:48.814][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-02 16:05:48.815][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-02 16:05:48.816][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-02 16:05:48.817][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-02 16:05:48.818][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-02 16:05:48.819][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-02 16:05:48.820][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-02 16:05:48.821][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-02 16:05:48.822][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-02 16:05:48.823][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-02 16:05:48.824][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-02 16:05:48.825][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-02 16:05:48.826][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-02 16:05:48.827][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-02 16:05:48.828][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-02 16:05:48.829][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-02 16:05:48.830][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-02 16:05:48.831][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-02 16:05:48.832][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-02 16:05:48.833][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-02 16:05:48.834][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-02 16:05:48.835][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-02 16:05:48.836][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-02 16:05:48.837][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-02 16:05:48.838][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-02 16:05:48.839][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-02 16:05:48.840][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-02 16:05:48.841][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-02 16:05:48.842][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-02 16:05:48.843][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-02 16:05:48.844][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-02 16:05:48.845][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-02 16:05:48.846][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-02 16:05:48.847][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-02 16:05:48.848][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-02 16:05:48.849][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-02 16:05:48.850][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-02 16:05:48.851][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-02 16:05:48.852][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-02 16:05:48.853][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-02 16:05:48.854][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-02 16:05:48.855][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-02 16:05:48.857][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-02 16:05:48.858][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-02 16:05:48.859][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-02 16:05:48.860][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-02 16:05:48.861][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-02 16:05:48.862][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-02 16:05:48.863][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-02 16:05:48.867][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-02 16:05:48.869][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-02 16:05:48.871][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-02 16:05:48.872][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:05:48.873][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.880][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 16:05:48.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.882][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.885][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 16:05:48.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.891][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.894][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 16:05:48.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.895][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.898][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 16:05:48.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.900][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.903][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 16:05:48.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.904][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.907][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 16:05:48.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.909][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.912][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 16:05:48.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.913][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.917][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 16:05:48.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.918][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.921][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 16:05:48.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.922][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.925][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 16:05:48.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.927][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.930][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 16:05:48.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.931][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.934][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 16:05:48.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.936][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.939][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 16:05:48.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.941][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.944][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 16:05:48.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.945][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.949][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 16:05:48.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.950][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.954][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 16:05:48.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.955][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:48.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.958][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 16:05:48.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.959][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 16:05:48.960][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-02 16:05:48.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-02 16:05:48.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:48.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:48.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:48.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:05:48.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:48.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-02 16:05:48.967][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-11-02 16:05:48.974][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:05:48.975][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.976][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.977][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.977][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-02 16:05:48.978][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.979][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-11-02 16:05:48.980][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.980][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.981][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-02 16:05:48.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-02 16:05:48.982][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.983][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-11-02 16:05:48.984][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-11-02 16:05:48.985][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-02 16:05:48.986][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-02 16:05:48.986][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-11-02 16:05:48.986][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-11-02 16:05:48.987][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-02 16:05:48.988][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.989][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-02 16:05:48.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-02 16:05:48.990][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-02 16:05:48.991][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-02 16:05:48.992][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-11-02 16:05:48.992][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-11-02 16:05:48.992][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-02 16:05:48.993][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-02 16:05:48.994][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-02 16:05:48.994][self$setPropertyValue]
biodb.DEBUG[2024-11-02 16:05:48.999][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-11-02 16:05:49.000][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-02 16:05:49.001][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-02 16:05:49.002][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-02 16:05:49.003][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-02 16:05:49.021][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:05:49.022][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-11-02 16:05:49.025][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-11-02 16:05:49.052][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-11-02 16:05:49.055][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 16:05:49.055][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-02 16:05:49.056][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-11-02 16:05:49.057][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-11-02 16:05:49.064][biodb::testThat]
biodb.INFO [2024-11-02 16:05:49.065][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-11-02 16:05:49.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:49.066][biodb::testThat]
biodb.TRACE[2024-11-02 16:05:49.069][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-11-02 16:05:49.071][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-02 16:05:49.073][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-02 16:05:49.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 16:05:49.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:49.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:49.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:49.092][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 16:05:49.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:49.093][FUN] Functions in observer BiodbConfig: [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 16:05:49.102][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.104][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.117][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.118][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.119][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.137][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.140][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.141][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.142][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.143][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.146][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.147][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.149][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.150][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.153][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.153][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.155][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.159][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.159][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.161][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.165][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.165][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.167][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.168][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.171][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.172][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.173][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.174][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.177][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.178][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.179][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.186][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.189][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.190][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.191][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.192][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.195][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.196][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.197][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.201][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.202][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.203][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.207][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.208][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.209][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.213][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.213][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.215][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.219][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.219][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.221][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.225][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.225][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.227][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.228][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.230][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.231][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.233][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.233][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.236][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:05:49.237][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.238][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.239][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:05:49.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.274][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.277][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.280][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.283][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.286][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.292][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.315][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.318][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.321][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.324][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.330][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.333][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.339][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.342][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.345][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.348][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.351][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.354][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.375][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.378][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.381][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.404][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.407][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.410][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.413][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.415][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.418][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.421][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.424][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.427][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.430][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:05:49.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.436][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.442][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:05:49.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.473][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.475][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.481][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:49.502][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-02 16:05:49.504][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:05:49.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:05:49.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.507][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:05:49.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:05:49.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.514][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:05:49.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:05:49.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.517][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:05:49.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:05:49.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.545][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.575][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.578][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:49.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.597][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.598][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.599][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.610][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.613][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.616][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.619][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.620][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.622][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.622][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:49.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.645][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.645][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.647][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:49.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.657][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.660][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.663][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.666][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.667][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.669][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.669][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:49.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.687][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.688][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.689][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:49.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.699][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.702][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.705][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.708][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.709][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.711][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:49.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.730][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.732][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:49.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:49.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.742][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.745][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.749][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.752][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.753][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.758][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:49.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:49.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.768][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.771][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.773][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.777][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.777][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.779][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.780][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:49.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:49.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.789][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.792][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.795][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.798][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.798][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.800][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.800][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.819][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.821][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:49.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.831][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.834][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.837][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.840][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.841][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.842][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.843][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:49.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.852][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.858][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.861][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.862][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.863][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.864][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:49.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.882][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.885][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.886][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.887][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:49.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.897][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.903][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.906][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.906][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.908][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.908][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:49.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:49.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.918][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.926][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.927][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.928][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:49.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.944][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.947][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.948][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.950][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:49.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.960][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.966][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.969][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.969][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.971][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.971][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.981][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:49.982][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:49.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.983][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.991][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.992][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:49.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.993][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:49.997][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.998][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:49.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:49.999][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.003][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.004][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.005][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.009][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.010][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.011][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.015][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.016][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.017][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.021][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.022][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.024][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.028][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.029][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.030][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.034][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.035][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.037][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.041][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:50.041][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:50.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.043][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.047][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:50.047][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:50.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.049][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.053][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.054][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.055][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.059][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.059][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.061][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.064][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.065][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.067][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.071][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.071][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.073][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.077][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.078][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.079][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.083][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.084][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.085][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.089][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:50.090][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:50.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.091][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 16:05:50.098][biodb::testThat]
biodb.INFO [2024-11-02 16:05:50.099][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-02 16:05:50.100][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:50.100][biodb::testThat]
biodb.DEBUG[2024-11-02 16:05:50.115][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-11-02 16:05:50.120][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-11-02 16:05:50.123][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.124][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-11-02 16:05:50.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-11-02 16:05:50.126][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-02 16:05:50.129][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-11-02 16:05:50.130][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-11-02 16:05:50.147][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-11-02 16:05:50.148][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-11-02 16:05:50.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-02 16:05:50.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:05:50.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:05:50.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:05:50.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:05:50.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:05:50.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-02 16:05:50.160][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.161][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.162][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.166][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.167][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.168][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.169][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.172][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.173][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.174][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.175][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.178][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.179][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.180][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.181][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.187][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.190][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.191][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.193][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.196][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.197][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.199][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.200][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.203][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.203][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.205][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.206][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.209][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.210][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.211][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.212][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.215][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.216][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.218][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.219][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.222][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:50.223][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:50.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.224][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:50.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:50.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.232][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:50.233][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:50.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.234][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.235][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:50.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:50.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.238][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.239][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.241][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.245][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.246][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.247][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.251][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.252][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.253][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.257][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.257][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.259][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.260][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.263][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:50.264][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:50.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.265][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:50.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:50.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.269][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:05:50.270][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.271][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.272][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-11-02 16:05:50.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.284][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.287][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.290][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-02 16:05:50.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.292][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.295][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.298][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-11-02 16:05:50.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-02 16:05:50.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-11-02 16:05:50.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.319][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.322][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.325][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-11-02 16:05:50.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.328][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.334][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-11-02 16:05:50.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.341][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.344][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-11-02 16:05:50.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.350][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.353][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.355][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:50.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:50.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.361][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:50.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:50.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-02 16:05:50.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-02 16:05:50.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:50.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:50.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:50.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:50.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-02 16:05:50.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-02 16:05:50.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.382][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.385][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.388][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.391][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-02 16:05:50.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-02 16:05:50.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.411][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.415][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.418][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-11-02 16:05:50.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.424][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.427][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.430][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:50.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:50.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.432][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:50.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:50.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.435][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-02 16:05:50.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-02 16:05:50.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.438][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:05:50.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.453][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-11-02 16:05:50.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-02 16:05:50.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.463][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.466][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.472][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:50.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:50.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.474][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:50.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:50.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.481][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:50.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-11-02 16:05:50.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-02 16:05:50.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-02 16:05:50.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.502][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-11-02 16:05:50.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-02 16:05:50.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-02 16:05:50.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-02 16:05:50.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-02 16:05:50.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-02 16:05:50.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-02 16:05:50.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 16:05:50.519][biodb::testThat]
biodb.INFO [2024-11-02 16:05:50.519][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-02 16:05:50.520][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:50.521][biodb::testThat]
biodb.TRACE[2024-11-02 16:05:50.523][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.524][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.525][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.526][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-11-02 16:05:50.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.551][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.554][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.562][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-11-02 16:05:50.563][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-11-02 16:05:50.564][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:05:50.565][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:05:50.566][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.567][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.568][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:05:50.569][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.570][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:05:50.571][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:05:50.571][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:05:50.572][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-02 16:05:50.573][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-02 16:05:50.574][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-02 16:05:50.574][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-02 16:05:50.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.587][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:05:50.588][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-02 16:05:50.589][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-11-02 16:05:50.600][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.601][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.603][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.604][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-11-02 16:05:50.614][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.618][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.621][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.626][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 16:05:50.667][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-11-02 16:05:50.668][private$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 16:05:50.669][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-11-02 16:05:50.679][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.680][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.681][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:05:50.683][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.683][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:05:50.694][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:05:50.695][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:05:50.696][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-02 16:05:50.697][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-02 16:05:50.697][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-02 16:05:50.698][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-02 16:05:50.700][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.703][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.706][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.709][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:05:50.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:05:50.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.712][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:05:50.713][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-02 16:05:50.713][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-11-02 16:05:50.724][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.725][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.726][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.727][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-11-02 16:05:50.738][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.742][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.745][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.750][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-11-02 16:05:50.751][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-11-02 16:05:50.752][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-11-02 16:05:50.752][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-11-02 16:05:50.754][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.755][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.756][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:05:50.757][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.758][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:05:50.759][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:05:50.760][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:05:50.760][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-02 16:05:50.761][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-02 16:05:50.762][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-02 16:05:50.762][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-02 16:05:50.764][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.771][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.774][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.777][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:05:50.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.780][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:05:50.781][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-11-02 16:05:50.782][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-11-02 16:05:50.802][biodb::testThat]
biodb.INFO [2024-11-02 16:05:50.804][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-11-02 16:05:50.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:50.835][biodb::testThat]
biodb.TRACE[2024-11-02 16:05:50.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.863][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-11-02 16:05:50.864][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:05:50.864][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-11-02 16:05:50.866][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.867][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.868][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-11-02 16:05:50.869][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-11-02 16:05:50.869][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-11-02 16:05:50.870][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-11-02 16:05:50.871][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-11-02 16:05:50.872][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-11-02 16:05:50.873][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-11-02 16:05:50.873][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-11-02 16:05:50.874][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-11-02 16:05:50.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.884][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:05:50.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:05:50.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-02 16:05:50.887][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-11-02 16:05:50.888][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-11-02 16:05:50.902][biodb::testThat]
biodb.INFO [2024-11-02 16:05:50.902][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-11-02 16:05:50.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:50.904][biodb::testThat]
biodb.TRACE[2024-11-02 16:05:50.920][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:05:50.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:05:50.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:05:50.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:05:50.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.930][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:05:50.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:05:50.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.933][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:05:50.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:05:50.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.966][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:05:50.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:05:50.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.970][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-02 16:05:50.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-02 16:05:50.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-02 16:05:50.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-02 16:05:50.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:05:50.975][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-02 16:05:50.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-02 16:05:50.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:05:50.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-02 16:05:50.984][biodb::testThat]
biodb.INFO [2024-11-02 16:05:50.984][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-02 16:05:50.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:50.986][biodb::testThat]
biodb.INFO [2024-11-02 16:05:50.992][biodb::testThat]
biodb.INFO [2024-11-02 16:05:50.993][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-02 16:05:50.994][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:50.995][biodb::testThat]
biodb.INFO [2024-11-02 16:05:51.001][biodb::testThat]
biodb.INFO [2024-11-02 16:05:51.002][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-02 16:05:51.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:05:51.003][biodb::testThat]
biodb.DEBUG[2024-11-02 16:05:51.006][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-11-02 16:06:08.701][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-11-02 16:06:08.737][biodb::testThat]
biodb.INFO [2024-11-02 16:06:08.738][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-02 16:06:08.738][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-02 16:06:08.739][biodb::testThat]
biodb.DEBUG[2024-11-02 16:06:11.852][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-11-02 16:06:11.875][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:06:11.876][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:06:11.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:06:11.877][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:06:11.878][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:06:11.879][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:06:11.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:06:11.880][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:06:11.881][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:06:11.882][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:06:11.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:06:11.883][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:06:11.884][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-02 16:06:11.885][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-02 16:06:11.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:06:11.886][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:06:11.887][ef$get] Asked field names are: description.
biodb.TRACE[2024-11-02 16:06:11.888][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-11-02 16:06:11.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:06:11.889][ef$get] fields variable is a list.
biodb.TRACE[2024-11-02 16:06:11.890][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-11-02 16:06:11.898][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-11-02 16:06:11.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-02 16:06:11.899][ef$get] fields variable is a list.
biodb.INFO [2024-11-02 16:06:11.900][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-02 16:06:11.901][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-11-02 16:06:11.902][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-11-02 16:06:11.902][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-02 16:06:11.903][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-02 16:06:11.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-02 16:06:11.904][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-02 16:06:11.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-02 16:06:11.906][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-02 16:06:11.906][FUN] Functions in observer 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 
  3.818   0.274  24.887

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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 ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 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: 1 WARNING, 1 NOTE
See
  ‘/Users/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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)