Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
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 8/33HostnameOS / ArchCHECK
biodbHmdb 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-22 09:55 -0400 (Sat, 22 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_19
git_last_commit: a7f41b2
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  WARNINGS  
palomino3Windows Server 2022 Datacenter / x64  WARNINGS  
merida1macOS 12.7.4 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on nebbiolo1

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: 1.10.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz
StartedAt: 2024-06-22 16:02:39 -0400 (Sat, 22 Jun 2024)
EndedAt: 2024-06-22 16:03:53 -0400 (Sat, 22 Jun 2024)
EllapsedTime: 74.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 2

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-06-22 16:03:48.388][biodb::testContext]
biodb.INFO [2024-06-22 16:03:48.391][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:03:48.391][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-22 16:03:48.392][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:03:48.393][biodb::testContext]
biodb.INFO [2024-06-22 16:03:48.399][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:03:48.401][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:03:48.408][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:48.409][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:03:48.410][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.413][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:03:48.430][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.433][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:03:48.434][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.438][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:03:48.438][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:03:48.439][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:03:48.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.443][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:03:48.444][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:03:48.444][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.448][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:03:48.449][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:03:48.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.452][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:03:48.453][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:03:48.454][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:03:48.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.457][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:03:48.458][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.461][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:03:48.462][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:03:48.463][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:03:48.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.466][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:03:48.467][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:03:48.468][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:03:48.469][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:03:48.470][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:03:48.471][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:03:48.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.474][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:03:48.475][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:03:48.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.478][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:03:48.479][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:03:48.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.482][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:03:48.483][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:03:48.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.487][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:03:48.488][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:03:48.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.490][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[2024-06-22 16:03:48.491][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:03:48.492][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:03:48.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.495][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:03:48.496][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:03:48.499][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:03:48.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.503][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:03:48.504][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:03:48.504][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:03:48.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.510][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:03:48.547][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.561][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-22 16:03:48.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:48.563][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.564][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.567][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:03:48.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:48.569][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.570][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:03:48.571][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:48.572][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.572][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.573][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:03:48.573][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:03:48.573][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:03:48.573][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:03:48.573][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:03:48.574][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:48.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.577][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:48.578][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.579][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.580][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.581][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:48.582][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:48.583][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.584][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.585][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:03:48.586][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.587][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:03:48.588][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.589][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:48.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.591][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.592][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.593][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.594][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:03:48.594][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:48.595][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.596][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:03:48.597][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:48.598][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.599][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.600][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:03:48.600][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:03:48.600][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:03:48.600][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:03:48.600][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:03:48.601][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:48.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:48.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.606][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.607][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.608][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:48.608][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:48.609][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.610][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.611][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:03:48.613][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.614][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-22 16:03:48.615][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:48.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.617][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.618][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.619][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.620][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:03:48.621][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:48.622][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.623][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:03:48.624][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:48.624][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.625][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.626][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.627][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:48.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.630][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:48.631][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.631][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.632][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.633][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.634][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:48.635][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:48.636][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.636][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.637][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:03:48.639][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.640][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:03:48.641][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.642][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:48.643][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.644][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.644][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.645][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.646][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:03:48.647][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:48.648][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.649][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:03:48.650][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:48.651][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.652][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:48.652][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.653][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:03:48.654][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.655][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.656][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:48.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:48.658][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:48.658][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:48.659][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.660][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:48.661][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:48.662][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:48.663][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:48.666][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:48.667][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.716][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[2024-06-22 16:03:48.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.733][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[2024-06-22 16:03:48.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.743][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[2024-06-22 16:03:48.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.749][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:03:48.754][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:03:48.756][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:03:48.757][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:03:48.759][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:03:48.760][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:03:48.761][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:03:48.763][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:03:48.764][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:03:48.766][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:03:48.767][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:03:48.768][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:03:48.770][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:03:48.771][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:03:48.773][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:03:48.774][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:03:48.775][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:03:48.777][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:03:48.778][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:03:48.780][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:03:48.781][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:03:48.782][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:03:48.784][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:03:48.785][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:03:48.787][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:03:48.788][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:03:48.789][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:03:48.791][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:03:48.792][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:03:48.794][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:03:48.795][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:03:48.796][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:03:48.798][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:03:48.799][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:03:48.801][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:03:48.802][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:03:48.804][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:03:48.805][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:03:48.806][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:03:48.808][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:03:48.809][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:03:48.811][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:03:48.812][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:03:48.813][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:03:48.815][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:03:48.816][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:03:48.818][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:03:48.819][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:03:48.820][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:03:48.822][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:03:48.823][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:03:48.825][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:03:48.826][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:03:48.827][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:03:48.829][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:03:48.830][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:03:48.832][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:03:48.833][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:03:48.834][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:03:48.836][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:03:48.837][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:03:48.838][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:03:48.840][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:03:48.841][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:03:48.843][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:03:48.844][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:03:48.845][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:03:48.847][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:03:48.848][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:03:48.849][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:03:48.851][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:03:48.852][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:03:48.854][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:03:48.855][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:03:48.856][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:03:48.858][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:03:48.859][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:03:48.860][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:03:48.862][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:03:48.863][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:03:48.864][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:03:48.866][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:03:48.867][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:03:48.873][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:03:48.875][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:03:48.879][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:03:48.880][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.881][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.909][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[2024-06-22 16:03:48.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.927][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[2024-06-22 16:03:48.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.955][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[2024-06-22 16:03:48.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:48.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:48.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:48.995][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:03:48.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:03:48.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:48.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:48.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:48.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:49.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:49.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:03:49.002][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-06-22 16:03:49.011][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-06-22 16:03:49.013][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:49.014][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-22 16:03:49.014][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:49.015][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:03:49.016][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:49.017][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-06-22 16:03:49.018][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:49.019][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:03:49.020][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-22 16:03:49.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:03:49.022][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:49.023][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-06-22 16:03:49.024][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-06-22 16:03:49.026][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:03:49.027][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:03:49.027][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-06-22 16:03:49.027][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-06-22 16:03:49.027][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:03:49.028][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:49.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:49.030][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:03:49.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:03:49.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:03:49.033][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:03:49.033][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-06-22 16:03:49.033][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-06-22 16:03:49.034][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:03:49.035][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:03:49.036][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:03:49.037][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:03:49.042][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-06-22 16:03:49.044][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:03:49.045][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:03:49.047][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:03:49.048][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:03:49.074][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-06-22 16:03:49.075][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-06-22 16:03:49.079][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-06-22 16:03:49.083][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-22 16:03:49.087][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:03:49.088][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:03:49.089][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-06-22 16:03:49.090][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-06-22 16:03:49.100][biodb::testThat]
biodb.INFO [2024-06-22 16:03:49.101][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-22 16:03:49.101][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:49.102][biodb::testThat]
biodb.TRACE[2024-06-22 16:03:49.106][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-06-22 16:03:49.108][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:03:49.111][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-22 16:03:49.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:03:49.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:49.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:49.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:49.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:49.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:49.135][FUN] Functions in observer BiodbConfig: [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[2024-06-22 16:03:49.147][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.148][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.150][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.166][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.167][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.169][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.193][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.197][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.198][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.200][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.201][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.205][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.206][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.207][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.209][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.212][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.213][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.215][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.220][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.221][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.223][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.227][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.228][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.230][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.231][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.235][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.271][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.273][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.275][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.278][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.279][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.281][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.282][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.286][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.287][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.289][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.290][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.293][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.294][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.297][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.301][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.302][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.303][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.308][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.309][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.311][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.316][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.317][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.319][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.323][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.324][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.326][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.327][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.331][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.332][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.333][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.334][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.338][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:49.339][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:49.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.341][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:49.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:49.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.346][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-06-22 16:03:49.347][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:49.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.348][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.349][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-06-22 16:03:49.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:49.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.393][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.401][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.404][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.408][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.411][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.415][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:49.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.444][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.447][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:49.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.451][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:49.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.462][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:49.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:49.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:49.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:49.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.469][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:49.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:49.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.473][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.480][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.483][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.487][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:49.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:49.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.516][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.519][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.523][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:49.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.555][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.559][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.562][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.566][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.569][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.573][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.577][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:49.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:49.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.580][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:49.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:49.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.584][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-22 16:03:49.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.591][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.598][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-22 16:03:49.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:49.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.636][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.639][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.646][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:49.675][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-06-22 16:03:49.678][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:49.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:49.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.681][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:49.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:49.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.685][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:49.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:49.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:49.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:49.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.720][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.750][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.754][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:49.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.778][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.779][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.781][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:49.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:49.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.792][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.795][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.799][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.803][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.808][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.810][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.811][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:49.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.832][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.832][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.834][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:49.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.845][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.849][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.852][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.856][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.857][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.859][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.859][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:49.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.880][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.881][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.883][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:49.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.894][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.898][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.901][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.905][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.906][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.907][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.908][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:49.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.929][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.930][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.931][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:49.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:49.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.946][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.950][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.957][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.958][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.959][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.960][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:49.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:49.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.970][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.977][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.981][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.982][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.984][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:49.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:49.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.994][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:49.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:49.998][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:49.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.001][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.005][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.006][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.008][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.009][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.029][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.030][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.032][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.046][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.050][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.053][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.054][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.056][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.057][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.066][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.074][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.081][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.082][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.084][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.095][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.105][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.106][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.108][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.109][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.119][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.123][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.126][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.130][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.131][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.132][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.133][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.154][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.155][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.156][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.178][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.179][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.191][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.195][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.198][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.206][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.207][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.208][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.209][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.219][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.220][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.221][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.222][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.225][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.226][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.228][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.232][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.233][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.234][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.238][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.239][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.241][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.244][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.245][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.247][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.251][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.252][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.253][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.257][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.258][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.263][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.264][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.266][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.269][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.270][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.272][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.276][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.277][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.278][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.282][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.283][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.285][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.288][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.289][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.290][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.291][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.294][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.295][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.297][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.302][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.303][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.307][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.308][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.310][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.313][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.314][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.316][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.319][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.320][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.322][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.326][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.327][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.332][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:03:50.338][biodb::testThat]
biodb.INFO [2024-06-22 16:03:50.339][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-22 16:03:50.340][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:50.341][biodb::testThat]
biodb.DEBUG[2024-06-22 16:03:50.353][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-06-22 16:03:50.360][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-06-22 16:03:50.365][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:50.366][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-06-22 16:03:50.368][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-06-22 16:03:50.369][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-22 16:03:50.371][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-06-22 16:03:50.372][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-06-22 16:03:50.393][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:03:50.394][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-22 16:03:50.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:03:50.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:50.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:50.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:50.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:50.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:50.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:03:50.407][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.408][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.410][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.415][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.416][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.417][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.418][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.422][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.423][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.425][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.426][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.430][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.431][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.432][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.433][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.437][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.438][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.440][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.444][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.445][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.447][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.452][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.453][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.455][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.456][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.459][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.465][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.467][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.468][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.471][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.472][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.474][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.475][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.479][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.480][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.481][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.486][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.487][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.489][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.494][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.495][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.496][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.501][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.502][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.504][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.505][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.509][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.510][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.511][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.516][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.517][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.519][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.523][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.524][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.526][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.527][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.531][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.532][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.533][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.535][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.538][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-06-22 16:03:50.539][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.541][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.542][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-06-22 16:03:50.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.557][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.560][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.564][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-22 16:03:50.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.568][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.571][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.575][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-22 16:03:50.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-22 16:03:50.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-22 16:03:50.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.604][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.607][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-22 16:03:50.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.615][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.618][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-22 16:03:50.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.626][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.629][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.633][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-22 16:03:50.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.636][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.640][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.643][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.647][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.651][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-22 16:03:50.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-22 16:03:50.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.661][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-22 16:03:50.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-22 16:03:50.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.679][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.683][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.687][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-22 16:03:50.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-22 16:03:50.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.712][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.719][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-22 16:03:50.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.727][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.730][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.734][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:50.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.737][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.741][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.745][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-22 16:03:50.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-22 16:03:50.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.748][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-22 16:03:50.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.763][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-22 16:03:50.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-22 16:03:50.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.786][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:50.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:50.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.790][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:50.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:50.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.797][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:50.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-22 16:03:50.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:03:50.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:03:50.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.822][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-06-22 16:03:50.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:03:50.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:03:50.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:03:50.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:03:50.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:03:50.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:03:50.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:03:50.840][biodb::testThat]
biodb.INFO [2024-06-22 16:03:50.841][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-22 16:03:50.842][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:50.842][biodb::testThat]
biodb.TRACE[2024-06-22 16:03:50.845][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.846][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.848][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.849][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-06-22 16:03:50.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.882][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.888][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-06-22 16:03:50.889][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-06-22 16:03:50.890][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-06-22 16:03:50.890][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-06-22 16:03:50.892][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:50.893][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:50.894][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-22 16:03:50.896][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:50.897][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-22 16:03:50.898][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-22 16:03:50.899][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-22 16:03:50.900][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-22 16:03:50.901][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-22 16:03:50.902][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-22 16:03:50.903][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-22 16:03:50.904][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:50.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:50.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.919][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-22 16:03:50.919][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-22 16:03:50.920][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-06-22 16:03:50.929][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.930][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.932][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.933][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-06-22 16:03:50.942][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.946][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:50.949][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:50.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:50.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:50.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:50.955][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[2024-06-22 16:03:51.007][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-06-22 16:03:51.008][private$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[2024-06-22 16:03:51.008][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-06-22 16:03:51.021][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.022][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.023][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-22 16:03:51.025][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.026][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-22 16:03:51.039][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-22 16:03:51.040][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-22 16:03:51.041][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-22 16:03:51.042][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-22 16:03:51.043][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-22 16:03:51.044][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-22 16:03:51.045][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:51.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:51.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.049][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:51.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:51.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.053][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:51.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:51.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.056][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:51.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:51.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:51.060][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-22 16:03:51.061][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-22 16:03:51.061][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-06-22 16:03:51.071][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.072][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.073][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:51.074][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-06-22 16:03:51.087][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.091][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.095][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:51.100][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-06-22 16:03:51.101][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-06-22 16:03:51.102][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-06-22 16:03:51.103][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-06-22 16:03:51.105][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.106][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.107][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-22 16:03:51.108][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.109][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-22 16:03:51.111][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-22 16:03:51.111][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-22 16:03:51.112][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-22 16:03:51.113][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-22 16:03:51.114][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-22 16:03:51.115][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-22 16:03:51.117][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.124][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.127][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:51.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:51.131][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-22 16:03:51.132][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-06-22 16:03:51.133][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-06-22 16:03:51.144][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.145][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-22 16:03:51.146][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.147][biodb::testThat]
biodb.TRACE[2024-06-22 16:03:51.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:51.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:51.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:51.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:51.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:51.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:51.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:51.176][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-06-22 16:03:51.177][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-06-22 16:03:51.178][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-06-22 16:03:51.179][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.180][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.182][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-06-22 16:03:51.183][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-22 16:03:51.184][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-06-22 16:03:51.185][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-06-22 16:03:51.186][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-06-22 16:03:51.187][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-06-22 16:03:51.188][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-06-22 16:03:51.189][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-06-22 16:03:51.190][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-06-22 16:03:51.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:51.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:51.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:51.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:51.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:51.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:51.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:51.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:51.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:03:51.206][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-06-22 16:03:51.207][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-06-22 16:03:51.223][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.223][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-22 16:03:51.224][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.225][biodb::testThat]
biodb.TRACE[2024-06-22 16:03:51.243][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.246][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.250][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:51.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:51.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.254][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:51.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:51.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.294][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:03:51.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.301][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:51.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:03:51.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:51.305][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:51.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:03:51.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:51.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:03:51.313][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.314][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-22 16:03:51.314][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.315][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.322][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.323][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-22 16:03:51.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.324][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.335][biodb::testThat]
biodb.INFO [2024-06-22 16:03:51.335][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-22 16:03:51.336][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:51.337][biodb::testThat]
biodb.DEBUG[2024-06-22 16:03:51.340][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-06-22 16:03:52.766][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-06-22 16:03:52.805][biodb::testThat]
biodb.INFO [2024-06-22 16:03:52.807][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-22 16:03:52.809][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:03:52.826][biodb::testThat]
biodb.DEBUG[2024-06-22 16:03:53.173][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-06-22 16:03:53.207][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:53.209][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:53.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:53.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:53.211][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:53.212][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:53.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:53.214][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:53.215][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:53.216][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:53.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:53.218][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:53.219][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:03:53.220][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:03:53.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:53.221][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:53.222][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-22 16:03:53.223][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-22 16:03:53.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:53.225][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:03:53.226][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:53.227][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-22 16:03:53.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:03:53.229][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:03:53.230][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:03:53.231][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-06-22 16:03:53.232][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-06-22 16:03:53.233][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:03:53.233][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:03:53.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:03:53.235][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:03:53.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:03:53.237][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:03:53.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 147 ]
> 
> proc.time()
   user  system elapsed 
  4.846   0.207   6.557

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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)