Back to Long Tests report for BioC 3.21

This page was generated on 2025-03-29 23:55 -0400 (Sat, 29 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4786
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4556
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4585
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 7/30HostnameOS / ArchCHECK
biodbHmdb 1.13.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-29 09:55 -0400 (Sat, 29 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: d2b9830
git_last_commit_date: 2024-10-29 11:06:39 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 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: 1.13.0
Command: /home/biocbuild/bbs-3.21-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_1.13.0.tar.gz
StartedAt: 2025-03-29 16:01:56 -0400 (Sat, 29 Mar 2025)
EndedAt: 2025-03-29 16:03:23 -0400 (Sat, 29 Mar 2025)
EllapsedTime: 87.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 2

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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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 [2025-03-29 16:02:57.379][biodb::testContext]
biodb.INFO [2025-03-29 16:02:57.381][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:02:57.382][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-29 16:02:57.383][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:02:57.384][biodb::testContext]
biodb.INFO [2025-03-29 16:02:57.389][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-29 16:02:57.391][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:02:57.398][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:57.399][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:02:57.400][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:02:57.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.403][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:02:57.420][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:02:57.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.424][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:02:57.425][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:02:57.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.428][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:02:57.429][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:02:57.430][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:02:57.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.433][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:02:57.434][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:02:57.435][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:02:57.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.439][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:02:57.440][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:02:57.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.442][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[2025-03-29 16:02:57.443][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:02:57.444][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:02:57.445][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:02:57.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.448][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:02:57.449][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:02:57.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.453][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:02:57.454][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:02:57.455][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:02:57.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.458][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:02:57.459][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:02:57.460][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:02:57.461][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:02:57.462][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:02:57.463][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:02:57.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.465][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[2025-03-29 16:02:57.466][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:02:57.467][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:02:57.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.471][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:02:57.472][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:02:57.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.475][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:02:57.476][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:02:57.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.480][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:02:57.481][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:02:57.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.485][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:02:57.486][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:02:57.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.489][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:02:57.490][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:02:57.494][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:02:57.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.498][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:02:57.499][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:02:57.500][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:02:57.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.506][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:02:57.538][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.560][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-29 16:02:57.561][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:57.564][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.565][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.567][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.567][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:02:57.569][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:57.570][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.571][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:02:57.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:57.573][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.574][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.575][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:57.575][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:02:57.575][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:02:57.575][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:02:57.575][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:02:57.576][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:57.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:57.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:57.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:57.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:57.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:57.581][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.582][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.583][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:57.584][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:57.585][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.586][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.587][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:02:57.589][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.590][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:02:57.591][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.592][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:57.593][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.594][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.595][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.596][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.597][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:02:57.598][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:57.599][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.600][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:02:57.601][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:57.602][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.602][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.603][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:57.603][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:02:57.603][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:02:57.603][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:02:57.603][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:02:57.604][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:57.605][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:57.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:57.607][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:57.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:57.609][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:57.610][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.611][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.612][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:57.613][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:57.613][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.614][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.616][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:02:57.617][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.618][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-29 16:02:57.619][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.620][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:57.621][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.622][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.623][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.624][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.625][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:02:57.626][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:57.627][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.628][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:02:57.629][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:57.630][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.631][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.632][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.633][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:57.634][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:57.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:57.636][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:57.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:57.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:57.639][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.640][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.641][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:57.642][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:57.642][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.643][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.645][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:02:57.646][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.647][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:02:57.648][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.649][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:57.650][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.651][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.652][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.653][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.654][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:02:57.655][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:57.656][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.657][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:02:57.658][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:57.659][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.660][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:57.661][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.662][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:57.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:57.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:57.665][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:57.666][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:57.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:57.668][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:57.668][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:57.670][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:57.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:57.672][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:57.676][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:57.677][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.704][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[2025-03-29 16:02:57.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.758][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:02:57.763][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:02:57.764][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:02:57.766][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:02:57.767][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:02:57.768][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:02:57.770][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:02:57.771][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:02:57.772][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:02:57.774][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:02:57.775][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:02:57.777][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:02:57.778][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:02:57.780][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:02:57.781][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:02:57.782][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:02:57.784][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:02:57.785][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:02:57.786][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:02:57.788][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:02:57.789][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:02:57.790][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:02:57.792][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:02:57.793][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:02:57.795][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:02:57.800][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:02:57.803][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:02:57.804][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:02:57.806][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:02:57.807][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:02:57.809][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:02:57.811][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:02:57.812][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:02:57.814][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:02:57.815][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:02:57.817][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:02:57.818][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:02:57.820][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:02:57.821][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:02:57.822][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:02:57.824][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:02:57.825][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:02:57.827][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:02:57.828][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:02:57.830][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:02:57.831][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:02:57.833][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:02:57.834][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:02:57.836][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:02:57.837][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:02:57.839][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:02:57.840][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:02:57.842][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:02:57.843][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:02:57.845][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:02:57.846][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:02:57.848][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:02:57.849][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:02:57.851][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:02:57.852][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:02:57.854][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:02:57.855][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:02:57.857][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:02:57.858][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:02:57.860][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:02:57.861][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:02:57.863][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:02:57.864][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:02:57.866][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:02:57.867][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:02:57.869][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:02:57.870][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:02:57.872][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:02:57.873][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:02:57.875][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:02:57.876][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:02:57.878][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:02:57.879][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:02:57.880][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:02:57.882][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:02:57.883][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:02:57.885][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:02:57.886][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:02:57.894][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:02:57.895][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-29 16:02:57.899][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:57.900][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.902][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.903][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[2025-03-29 16:02:57.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.932][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[2025-03-29 16:02:57.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.972][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[2025-03-29 16:02:57.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:57.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:57.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:57.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:57.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:57.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:57.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:57.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:58.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:58.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:58.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:58.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:58.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:58.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:58.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:58.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:58.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:58.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:58.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:58.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:58.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:58.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:58.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:58.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:58.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:58.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:58.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:58.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:58.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:58.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:58.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:58.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:58.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:58.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:58.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:58.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:58.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:58.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:58.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:58.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:58.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:58.028][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:02:58.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:58.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:58.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:58.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:58.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:58.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:58.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:58.036][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-29 16:02:58.045][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-29 16:02:58.047][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:58.048][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-29 16:02:58.049][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:58.050][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:58.051][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:58.052][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-29 16:02:58.053][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:58.054][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:58.055][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-29 16:02:58.056][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:58.057][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:58.058][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-29 16:02:58.059][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-29 16:02:58.061][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:58.062][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:58.062][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-29 16:02:58.062][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-29 16:02:58.063][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:02:58.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:58.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:58.065][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:58.066][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:58.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:58.068][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:58.069][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-29 16:02:58.069][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-29 16:02:58.070][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:58.071][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:58.072][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:58.073][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:58.078][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-29 16:02:58.079][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:02:58.081][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:02:58.082][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:02:58.084][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:02:58.105][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-29 16:02:58.106][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-29 16:02:58.135][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-29 16:02:58.139][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-29 16:02:58.143][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:02:58.143][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:02:58.145][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-29 16:02:58.146][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-03-29 16:02:58.154][biodb::testThat]
biodb.INFO [2025-03-29 16:02:58.155][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-29 16:02:58.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:58.156][biodb::testThat]
biodb.TRACE[2025-03-29 16:02:58.160][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-03-29 16:02:58.161][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:02:58.165][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-29 16:02:58.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:02:58.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:58.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:58.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:58.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:58.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:58.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:02:58.197][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.198][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.200][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.217][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.218][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.219][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.243][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.247][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.248][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.251][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.255][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.256][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.258][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.259][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.263][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.264][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.271][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.272][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.274][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.279][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.280][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.282][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.283][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.287][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.288][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.291][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.295][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.302][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.304][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.309][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.310][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.312][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.313][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.317][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:58.318][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:58.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.321][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:58.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:58.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.325][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:58.326][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:58.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:58.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:58.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.333][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.334][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.340][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.341][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.348][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.349][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.351][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.356][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:58.357][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:58.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.359][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.360][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:58.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:58.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.364][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:58.365][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:58.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:58.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:58.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.371][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-29 16:02:58.372][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:58.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.374][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.375][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-29 16:02:58.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:58.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.421][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.425][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.428][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:58.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.435][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.439][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.443][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.469][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.477][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:58.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.481][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.488][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:58.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:58.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:58.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.496][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:58.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:58.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.500][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:58.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:58.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.503][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:58.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:58.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:58.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:58.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.511][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:58.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:58.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.515][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:58.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:58.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:58.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:58.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.522][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:58.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:58.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:58.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:58.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:58.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:58.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:58.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:58.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.549][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.552][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.556][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:58.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.586][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.589][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.593][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.597][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.601][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.604][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:58.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.612][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:58.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:58.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.616][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:58.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:58.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.619][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-29 16:02:58.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.631][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.634][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-29 16:02:58.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:58.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.673][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.677][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.685][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:58.711][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-29 16:02:58.717][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:58.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.721][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:58.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:58.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.724][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:58.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:58.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.728][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:58.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:58.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.760][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.799][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:58.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.820][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.821][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.823][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:58.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:58.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.834][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.838][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.841][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.845][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.846][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.849][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:58.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.874][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.875][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:58.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.888][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.892][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.895][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.899][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.900][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.903][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:58.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.924][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.925][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.927][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:58.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.937][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.941][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.945][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.949][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.950][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.951][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.952][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:58.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.973][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.976][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:58.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:58.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.987][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:58.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:58.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.994][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:58.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:58.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:58.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:58.998][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:58.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.001][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:59.002][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.004][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.005][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:59.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.015][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.019][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.026][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.027][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.030][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.040][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.043][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.047][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.051][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.052][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.054][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.055][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.076][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.077][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.097][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.100][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.101][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.104][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.114][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.118][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.121][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.128][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.129][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.131][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.132][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.142][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.146][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.149][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.153][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.154][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.156][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.167][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.170][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.174][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.178][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.179][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.182][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.191][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.203][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.204][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.205][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.216][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.228][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.230][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.241][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.245][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.248][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.252][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.253][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.256][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.269][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.270][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.272][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.275][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.276][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.278][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.282][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.283][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.288][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.289][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.295][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.296][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.298][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.301][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.302][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.304][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.308][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.309][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.311][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.315][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.316][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.317][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.321][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:59.322][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.324][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.328][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.334][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.335][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.337][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.341][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.342][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.344][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.347][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.348][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.354][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.355][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.357][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.360][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.361][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.362][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.363][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.367][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.368][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.373][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.374][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.376][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.380][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.381][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.383][ef$get] fields variable is a list.
biodb.INFO [2025-03-29 16:02:59.389][biodb::testThat]
biodb.INFO [2025-03-29 16:02:59.390][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-29 16:02:59.391][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:59.395][biodb::testThat]
biodb.DEBUG[2025-03-29 16:02:59.408][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-29 16:02:59.415][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-29 16:02:59.418][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:02:59.420][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-29 16:02:59.422][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-29 16:02:59.423][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-29 16:02:59.425][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-29 16:02:59.426][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-29 16:02:59.448][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:02:59.449][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-29 16:02:59.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:02:59.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:59.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:59.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:59.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:59.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:59.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:02:59.462][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.463][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.465][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.470][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.471][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.474][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.478][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.479][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.480][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.481][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.482][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.486][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.487][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.488][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.490][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.494][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.496][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.501][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.502][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.509][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.510][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.512][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.513][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.517][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.518][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.521][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.525][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.526][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.537][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.538][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.540][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.541][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.545][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.548][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.549][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.553][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.554][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.556][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.561][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.562][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.563][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.568][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.569][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.570][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.571][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.576][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.577][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.578][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.579][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.584][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:59.585][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.587][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.588][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:59.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.591][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.592][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.595][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.599][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-29 16:02:59.600][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.602][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-29 16:02:59.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.618][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.622][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.626][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-29 16:02:59.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.630][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.633][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.637][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-29 16:02:59.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-29 16:02:59.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-29 16:02:59.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.663][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.670][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.674][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-29 16:02:59.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.678][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.681][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.685][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-29 16:02:59.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.689][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.692][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-29 16:02:59.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.700][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:59.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.704][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:59.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.707][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:02:59.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:02:59.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.715][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-29 16:02:59.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-29 16:02:59.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-29 16:02:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-29 16:02:59.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.737][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.745][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.748][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.752][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-29 16:02:59.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-29 16:02:59.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.778][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.782][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.786][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-29 16:02:59.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.789][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.793][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.800][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:02:59.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.804][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.808][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.812][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-29 16:02:59.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-29 16:02:59.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.815][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-29 16:02:59.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.830][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-29 16:02:59.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-29 16:02:59.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.835][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.854][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:59.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:59.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.857][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:59.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:59.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.865][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:59.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-29 16:02:59.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:59.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:59.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:59.891][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-29 16:02:59.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:02:59.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:02:59.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:02:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:02:59.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:02:59.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:02:59.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:02:59.909][biodb::testThat]
biodb.INFO [2025-03-29 16:02:59.910][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-29 16:02:59.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:59.912][biodb::testThat]
biodb.TRACE[2025-03-29 16:02:59.914][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.915][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.917][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:59.918][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-03-29 16:02:59.944][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:59.957][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-03-29 16:02:59.959][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-29 16:02:59.959][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-29 16:02:59.960][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-29 16:02:59.962][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:02:59.963][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:02:59.965][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-29 16:02:59.966][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:02:59.967][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-29 16:02:59.968][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-29 16:02:59.969][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-29 16:02:59.970][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-29 16:02:59.971][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-29 16:02:59.972][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-29 16:02:59.973][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-29 16:02:59.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.982][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:59.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:59.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:59.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:59.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:59.989][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-29 16:02:59.990][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-29 16:02:59.991][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-29 16:03:00.000][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:00.001][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:00.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.003][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:00.004][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-03-29 16:03:00.014][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:00.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:00.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.017][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:00.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:00.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.021][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:00.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:00.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:00.027][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[2025-03-29 16:03:00.079][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-29 16:03:00.080][private$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[2025-03-29 16:03:00.081][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-03-29 16:03:00.094][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.095][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.096][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-29 16:03:00.097][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.098][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-29 16:03:00.112][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-29 16:03:00.113][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-29 16:03:00.114][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-29 16:03:00.115][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-29 16:03:00.116][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-29 16:03:00.117][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-29 16:03:00.119][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:00.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:00.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.122][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:00.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:00.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.126][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:00.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:00.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.130][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:00.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:00.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:00.134][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-29 16:03:00.134][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-29 16:03:00.135][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-29 16:03:00.145][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.146][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.148][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:00.149][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-03-29 16:03:00.158][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.162][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.166][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:00.175][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-03-29 16:03:00.176][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-03-29 16:03:00.177][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-29 16:03:00.178][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-29 16:03:00.179][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.181][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.182][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-29 16:03:00.183][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.184][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-29 16:03:00.185][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-29 16:03:00.186][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-29 16:03:00.187][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-29 16:03:00.188][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-29 16:03:00.189][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-29 16:03:00.190][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-29 16:03:00.192][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.195][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.199][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.203][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:00.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:00.207][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-29 16:03:00.207][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-29 16:03:00.208][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-03-29 16:03:00.220][biodb::testThat]
biodb.INFO [2025-03-29 16:03:00.221][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-29 16:03:00.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:00.223][biodb::testThat]
biodb.TRACE[2025-03-29 16:03:00.232][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:00.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:00.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.235][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:00.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:00.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.239][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:00.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:00.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:00.251][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-29 16:03:00.252][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-29 16:03:00.253][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-29 16:03:00.255][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.256][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.257][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-29 16:03:00.259][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-29 16:03:00.260][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-29 16:03:00.261][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-29 16:03:00.262][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-29 16:03:00.263][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-29 16:03:00.264][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-29 16:03:00.265][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-29 16:03:00.265][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-29 16:03:00.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:00.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:00.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:00.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:00.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:00.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:00.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:00.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:00.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:03:00.282][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-29 16:03:00.283][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-03-29 16:03:00.295][biodb::testThat]
biodb.INFO [2025-03-29 16:03:00.296][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-29 16:03:00.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:00.297][biodb::testThat]
biodb.TRACE[2025-03-29 16:03:00.319][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:00.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:00.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.322][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:00.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:00.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.326][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:00.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:00.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.330][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:00.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:00.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.371][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:00.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:00.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.375][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:03:00.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:03:00.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.378][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:00.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:03:00.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:00.382][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:00.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:03:00.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:00.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:00.390][biodb::testThat]
biodb.INFO [2025-03-29 16:03:00.391][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-29 16:03:00.392][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:00.393][biodb::testThat]
biodb.INFO [2025-03-29 16:03:00.400][biodb::testThat]
biodb.INFO [2025-03-29 16:03:00.400][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-29 16:03:00.401][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:00.402][biodb::testThat]
biodb.INFO [2025-03-29 16:03:00.408][biodb::testThat]
biodb.INFO [2025-03-29 16:03:00.409][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-29 16:03:00.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:00.411][biodb::testThat]
biodb.DEBUG[2025-03-29 16:03:00.417][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-03-29 16:03:18.981][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-03-29 16:03:19.037][biodb::testThat]
biodb.INFO [2025-03-29 16:03:19.040][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-29 16:03:19.042][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:03:19.044][biodb::testThat]
biodb.DEBUG[2025-03-29 16:03:22.903][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-03-29 16:03:22.954][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:22.962][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:22.964][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:22.967][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:22.969][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:22.971][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:22.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:22.975][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:22.977][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:22.979][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:22.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:22.983][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:22.985][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:03:22.986][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:03:22.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:22.989][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:22.991][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-29 16:03:22.992][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-29 16:03:22.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:22.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:03:22.997][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:22.998][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-29 16:03:22.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:03:23.001][ef$get] fields variable is a list.
biodb.INFO [2025-03-29 16:03:23.002][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:03:23.004][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-29 16:03:23.005][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-29 16:03:23.006][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:03:23.007][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:03:23.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:03:23.009][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:03:23.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:03:23.011][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:03:23.012][FUN] Functions in observer 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 
  4.744   0.282  27.253

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 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 ‘1.13.0’
* 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-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... 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-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.13.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)