Back to Long Tests report for BioC 3.20

This page was generated on 2024-12-21 23:55 -0500 (Sat, 21 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/32HostnameOS / ArchCHECK
biodbHmdb 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-12-21 09:55 -0500 (Sat, 21 Dec 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_20
git_last_commit: 0eb718c
git_last_commit_date: 2024-10-29 11:06:39 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on merida1

To the developers/maintainers of the biodbHmdb package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbHmdb
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.12.0.tar.gz
StartedAt: 2024-12-21 16:01:21 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 16:30:07 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 1726.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 1

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-12-21 16:02:41.988][biodb::testContext]
biodb.INFO [2024-12-21 16:02:41.992][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-21 16:02:41.993][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-12-21 16:02:41.994][biodb::testContext] ********************************************************************************
biodb.INFO [2024-12-21 16:02:41.995][biodb::testContext]
biodb.INFO [2024-12-21 16:02:42.002][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-12-21 16:02:42.004][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-12-21 16:02:42.012][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-21 16:02:42.014][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-12-21 16:02:42.015][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-12-21 16:02:42.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.020][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-12-21 16:02:42.045][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-12-21 16:02:42.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.050][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-12-21 16:02:42.051][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-12-21 16:02:42.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.056][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-12-21 16:02:42.057][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-12-21 16:02:42.058][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-12-21 16:02:42.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.063][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-12-21 16:02:42.064][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-12-21 16:02:42.065][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-12-21 16:02:42.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.070][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-12-21 16:02:42.071][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-12-21 16:02:42.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.076][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-12-21 16:02:42.077][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-12-21 16:02:42.078][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-12-21 16:02:42.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.083][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-12-21 16:02:42.084][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-12-21 16:02:42.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.089][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-12-21 16:02:42.090][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-12-21 16:02:42.091][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-12-21 16:02:42.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.096][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-12-21 16:02:42.097][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-12-21 16:02:42.098][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-12-21 16:02:42.099][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-12-21 16:02:42.101][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-12-21 16:02:42.102][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-12-21 16:02:42.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.106][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-12-21 16:02:42.108][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-12-21 16:02:42.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.112][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-12-21 16:02:42.114][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-12-21 16:02:42.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.118][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-12-21 16:02:42.119][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-12-21 16:02:42.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.124][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-12-21 16:02:42.125][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-21 16:02:42.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.130][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-12-21 16:02:42.131][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-12-21 16:02:42.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.136][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-12-21 16:02:42.137][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-12-21 16:02:42.148][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-12-21 16:02:42.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.153][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-12-21 16:02:42.154][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-12-21 16:02:42.156][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-12-21 16:02:42.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.163][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-12-21 16:02:42.208][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.236][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-12-21 16:02:42.237][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.238][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-21 16:02:42.240][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.241][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.242][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.243][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.245][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-21 16:02:42.246][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-21 16:02:42.247][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.248][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-12-21 16:02:42.250][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-21 16:02:42.251][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.252][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.253][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-21 16:02:42.253][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-21 16:02:42.253][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-21 16:02:42.253][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-21 16:02:42.253][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-21 16:02:42.255][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-21 16:02:42.256][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.257][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.258][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-21 16:02:42.260][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.261][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.262][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.263][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.264][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-21 16:02:42.265][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-21 16:02:42.267][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.268][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.269][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-12-21 16:02:42.272][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.273][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-12-21 16:02:42.274][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.275][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-21 16:02:42.277][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.278][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.279][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.280][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.282][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-21 16:02:42.283][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-21 16:02:42.284][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.285][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-12-21 16:02:42.287][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-21 16:02:42.288][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.289][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.290][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-21 16:02:42.290][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-12-21 16:02:42.290][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-12-21 16:02:42.290][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-12-21 16:02:42.290][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-12-21 16:02:42.292][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-21 16:02:42.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.295][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-21 16:02:42.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.299][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.300][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.301][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-21 16:02:42.302][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-21 16:02:42.303][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.305][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.306][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-12-21 16:02:42.308][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.310][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-12-21 16:02:42.311][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.312][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-21 16:02:42.313][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.315][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.316][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.317][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.318][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-12-21 16:02:42.320][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-21 16:02:42.321][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.322][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-12-21 16:02:42.323][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-21 16:02:42.325][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.326][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.327][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.328][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-21 16:02:42.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-21 16:02:42.333][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.334][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.335][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.337][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.338][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-21 16:02:42.339][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-21 16:02:42.340][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.341][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.343][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-12-21 16:02:42.345][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.346][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-12-21 16:02:42.348][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.349][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-21 16:02:42.350][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.351][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.353][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.354][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.355][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-12-21 16:02:42.356][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-21 16:02:42.358][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.359][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-12-21 16:02:42.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-21 16:02:42.361][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.363][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.364][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.365][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-12-21 16:02:42.366][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.369][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-21 16:02:42.370][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.371][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.372][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.374][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.375][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-21 16:02:42.376][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-21 16:02:42.377][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.379][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.383][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-21 16:02:42.384][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.402][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[2024-12-21 16:02:42.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.452][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[2024-12-21 16:02:42.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.457][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[2024-12-21 16:02:42.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.474][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[2024-12-21 16:02:42.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.486][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-12-21 16:02:42.491][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-12-21 16:02:42.493][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-12-21 16:02:42.495][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-12-21 16:02:42.496][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-12-21 16:02:42.498][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-21 16:02:42.500][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-12-21 16:02:42.501][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-12-21 16:02:42.503][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-12-21 16:02:42.505][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-21 16:02:42.507][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-21 16:02:42.508][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-12-21 16:02:42.510][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-12-21 16:02:42.512][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-12-21 16:02:42.514][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-12-21 16:02:42.515][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-21 16:02:42.517][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-12-21 16:02:42.519][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-12-21 16:02:42.520][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-12-21 16:02:42.522][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-12-21 16:02:42.524][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-12-21 16:02:42.526][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-12-21 16:02:42.527][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-12-21 16:02:42.529][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-12-21 16:02:42.531][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-12-21 16:02:42.533][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-12-21 16:02:42.534][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-12-21 16:02:42.536][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-12-21 16:02:42.538][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-12-21 16:02:42.540][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-12-21 16:02:42.541][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-12-21 16:02:42.543][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-12-21 16:02:42.545][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-12-21 16:02:42.546][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-12-21 16:02:42.548][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-12-21 16:02:42.550][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-12-21 16:02:42.552][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-12-21 16:02:42.553][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-12-21 16:02:42.555][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-12-21 16:02:42.557][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-12-21 16:02:42.558][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-12-21 16:02:42.560][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-12-21 16:02:42.562][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-12-21 16:02:42.564][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-12-21 16:02:42.565][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-12-21 16:02:42.567][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-12-21 16:02:42.569][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-12-21 16:02:42.571][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-12-21 16:02:42.572][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-12-21 16:02:42.574][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-12-21 16:02:42.576][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-12-21 16:02:42.577][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-12-21 16:02:42.579][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-12-21 16:02:42.581][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-12-21 16:02:42.583][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-12-21 16:02:42.584][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-12-21 16:02:42.586][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-12-21 16:02:42.588][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-12-21 16:02:42.590][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-12-21 16:02:42.591][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-12-21 16:02:42.593][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-12-21 16:02:42.595][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-12-21 16:02:42.596][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-12-21 16:02:42.598][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-12-21 16:02:42.600][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-12-21 16:02:42.602][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-12-21 16:02:42.603][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-12-21 16:02:42.605][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-12-21 16:02:42.607][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-12-21 16:02:42.608][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-12-21 16:02:42.610][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-12-21 16:02:42.612][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-12-21 16:02:42.614][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-12-21 16:02:42.615][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-12-21 16:02:42.617][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-12-21 16:02:42.619][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-12-21 16:02:42.621][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-12-21 16:02:42.622][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-12-21 16:02:42.624][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-12-21 16:02:42.626][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-12-21 16:02:42.627][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-12-21 16:02:42.629][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-12-21 16:02:42.631][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-12-21 16:02:42.638][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-12-21 16:02:42.640][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-12-21 16:02:42.644][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-12-21 16:02:42.645][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.647][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.682][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[2024-12-21 16:02:42.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.713][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[2024-12-21 16:02:42.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.744][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[2024-12-21 16:02:42.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.793][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-12-21 16:02:42.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-12-21 16:02:42.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:42.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:42.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-12-21 16:02:42.803][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-12-21 16:02:42.817][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-12-21 16:02:42.819][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.821][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.822][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.823][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-12-21 16:02:42.824][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.826][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-12-21 16:02:42.827][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.828][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.830][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-12-21 16:02:42.831][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-12-21 16:02:42.832][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.834][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-12-21 16:02:42.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-12-21 16:02:42.836][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-12-21 16:02:42.838][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-12-21 16:02:42.839][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-12-21 16:02:42.839][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-12-21 16:02:42.839][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-12-21 16:02:42.840][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-12-21 16:02:42.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.844][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-12-21 16:02:42.845][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-12-21 16:02:42.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-12-21 16:02:42.848][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-12-21 16:02:42.849][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-12-21 16:02:42.849][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-12-21 16:02:42.850][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-12-21 16:02:42.852][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-12-21 16:02:42.853][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-12-21 16:02:42.854][self$setPropertyValue]
biodb.DEBUG[2024-12-21 16:02:42.862][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-12-21 16:02:42.864][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-12-21 16:02:42.866][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-12-21 16:02:42.868][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-12-21 16:02:42.870][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-12-21 16:02:42.893][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-12-21 16:02:42.894][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-12-21 16:02:42.925][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-12-21 16:02:42.930][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-12-21 16:02:42.935][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-21 16:02:42.936][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-12-21 16:02:42.938][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-12-21 16:02:42.939][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-12-21 16:02:42.951][biodb::testThat]
biodb.INFO [2024-12-21 16:02:42.952][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-12-21 16:02:42.953][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:02:42.954][biodb::testThat]
biodb.TRACE[2024-12-21 16:02:42.959][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-12-21 16:02:42.962][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-12-21 16:02:42.967][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-12-21 16:02:42.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-21 16:02:42.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:02:42.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:02:42.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:02:42.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:02:43.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:02:43.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-21 16:02:43.013][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.015][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.017][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.041][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.042][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.045][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.081][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.087][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.088][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.091][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.092][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.098][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.099][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.101][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.103][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.108][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.110][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.112][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.119][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.120][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.123][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.129][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.131][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.133][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.135][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.140][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.141][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.144][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.145][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.150][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.152][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.162][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.163][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.168][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.170][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.172][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.174][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.179][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:43.180][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:43.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.183][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:43.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:43.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.189][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:43.191][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:43.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.193][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:43.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:43.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.200][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.201][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.203][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.205][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.210][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.212][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.214][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.221][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.222][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.224][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.231][ef$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:43.232][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:43.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.235][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.236][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:43.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:43.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.241][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:43.242][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:43.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.245][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.246][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:43.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:43.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.251][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-12-21 16:02:43.253][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:43.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.255][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.257][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-12-21 16:02:43.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:43.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.321][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.326][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.331][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:43.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.336][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.344][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.349][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:43.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.384][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.389][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.394][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:43.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.398][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.403][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.408][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:43.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.413][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:43.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:43.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.418][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:43.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:43.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.423][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:43.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:43.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.428][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:43.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:43.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.433][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:43.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:43.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.438][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:43.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:43.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:43.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:43.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:43.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:43.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.452][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:43.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:43.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:43.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:43.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:43.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:43.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:43.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:43.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.487][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.492][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.497][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:43.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:43.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.535][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.540][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.550][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.555][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.560][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.565][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:43.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:43.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:43.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:43.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.575][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:43.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:43.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.579][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-12-21 16:02:43.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.599][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-12-21 16:02:43.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:43.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.628][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:43.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:43.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.652][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.657][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.667][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:02:43.702][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-12-21 16:02:43.705][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-21 16:02:43.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-21 16:02:43.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.714][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-21 16:02:43.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-21 16:02:43.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.719][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-21 16:02:43.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-21 16:02:43.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.724][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-21 16:02:43.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-21 16:02:43.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.769][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.812][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.817][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.822][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:02:43.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.851][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.852][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.855][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:43.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:43.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.871][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.877][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.882][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.887][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.888][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.890][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.892][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:43.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.927][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.928][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.930][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:43.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.946][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.951][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.956][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.961][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.963][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.965][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.966][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:43.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:43.996][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.997][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:43.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:43.999][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:44.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:44.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.016][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.021][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.026][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.031][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.032][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.034][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.036][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:44.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:44.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:44.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:44.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:44.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:44.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.065][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:44.067][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:44.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.069][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:44.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:44.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.085][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:44.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:44.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.090][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:44.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:44.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.100][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:44.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:44.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.105][ef$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:44.106][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:44.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.108][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.109][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:44.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:44.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:44.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:44.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:44.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:44.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:44.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:44.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.139][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:44.141][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:44.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.143][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.144][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:44.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:44.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.159][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.164][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.169][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.174][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.175][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.177][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.178][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.208][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.209][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.212][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.228][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.233][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.243][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.244][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.246][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.262][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.267][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.272][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.277][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.279][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.285][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.286][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.301][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.311][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.316][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.317][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.320][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.321][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.335][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:44.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:44.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.340][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:44.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:44.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.345][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:44.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:44.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:44.352][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:44.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.354][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.355][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:44.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:44.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:44.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:44.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:44.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:44.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:44.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:44.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.385][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:44.386][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:44.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.388][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:44.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:44.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.419][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.421][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.423][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.439][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.444][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.449][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.454][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.455][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.458][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.459][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.478][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:02:44.480][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:02:44.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.482][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.488][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.490][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:02:44.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.492][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.499][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.500][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:02:44.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.502][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.509][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:02:44.510][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:02:44.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.513][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.519][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:44.520][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:02:44.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.523][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.529][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.530][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:02:44.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.533][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.539][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.540][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:02:44.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.543][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.549][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.550][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:02:44.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.553][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.559][ef$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:02:44.560][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:02:44.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.563][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.569][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:02:44.570][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:02:44.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.573][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.579][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:02:44.580][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:02:44.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.583][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.589][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.590][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:02:44.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.593][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.599][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.601][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:02:44.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.603][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.609][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.611][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:02:44.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.613][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.619][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:02:44.620][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:02:44.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.623][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.629][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:44.630][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:02:44.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.633][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.639][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:44.641][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:02:44.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.643][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:02:44.649][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:02:44.651][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:02:44.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:02:44.653][ef$get] fields variable is a list.
biodb.INFO [2024-12-21 16:02:44.664][biodb::testThat]
biodb.INFO [2024-12-21 16:02:44.665][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-12-21 16:02:44.666][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:02:44.667][biodb::testThat]
biodb.DEBUG[2024-12-21 16:02:44.697][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-12-21 16:02:44.711][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-12-21 16:02:44.719][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-12-21 16:02:44.723][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-12-21 16:02:44.726][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-12-21 16:02:44.728][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-12-21 16:02:44.733][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
==================================================
downloaded 909.7 MB

biodb.TRACE[2024-12-21 16:05:58.726][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb.metabolitese06c79e273a5zip".
biodb.TRACE[2024-12-21 16:05:58.727][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-12-21 16:05:58.729][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-12-21 16:05:58.731][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-12-21 16:05:58.732][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-12-21 16:05:58.735][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markere06c2169427marker".
biodb.TRACE[2024-12-21 16:05:58.736][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-12-21 16:05:58.738][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-12-21 16:05:58.740][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-12-21 16:05:58.742][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-12-21 16:05:58.743][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-12-21 16:05:58.745][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-12-21 16:05:58.746][private$doExtractDownload] Unzipping /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp...
biodb.DEBUG[2024-12-21 16:06:46.907][private$findXmlDatabaseFile] Found files [1]: "hmdb_metabolites.xml" into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-12-21 16:06:46.908][private$findXmlDatabaseFile] Found XML file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_metabolites.xml in ZIP file.
biodb.DEBUG[2024-12-21 16:06:46.910][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-12-21 16:06:46.912][private$doExtractDownload] Extract entries from XML file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_metabolites.xml", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2024-12-21 16:27:47.716][self$addFilesToCache] Moving files to cache [217920]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000002.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000005.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000008.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000010.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000011.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000012.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000014.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000015.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000016.xml, ...".
biodb.TRACE[2024-12-21 16:27:48.603][private$doAddFilesToCache] Destination files are [217920]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000005.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000008.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000010.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000011.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000012.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000014.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000015.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000016.xml, ...".
biodb.DEBUG[2024-12-21 16:29:49.036][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-12-21 16:29:49.038][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-12-21 16:29:49.784][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markere06c18588d83marker".
biodb.TRACE[2024-12-21 16:29:49.786][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-12-21 16:29:49.788][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-12-21 16:29:49.790][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-12-21 16:29:49.792][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-12-21 16:29:49.795][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-12-21 16:29:49.797][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-12-21 16:29:49.837][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-12-21 16:29:49.839][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-12-21 16:29:49.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-12-21 16:29:49.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:29:49.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:29:49.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:29:49.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:29:49.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:29:49.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-12-21 16:29:49.866][ef$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:49.868][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:49.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.870][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:49.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:49.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.878][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:49.879][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:49.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.882][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.884][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:49.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:49.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.890][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:29:49.892][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:29:49.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.894][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.896][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:29:49.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:29:49.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.901][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:29:49.903][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:29:49.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.905][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.907][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:29:49.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:29:49.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.913][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:29:49.914][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:29:49.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.917][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:29:49.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:29:49.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.924][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:49.926][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:49.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.928][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:49.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:49.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.936][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:49.938][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:49.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.940][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.942][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:49.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:49.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.948][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:49.949][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:49.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.951][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:49.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.959][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:49.962][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:49.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.965][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.967][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:49.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:49.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.973][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:49.975][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:49.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.979][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.981][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:49.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:49.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.988][ef$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:29:49.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:29:49.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:49.994][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:49.996][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:29:49.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:29:49.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.002][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:29:50.004][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:29:50.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.007][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:29:50.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:29:50.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.015][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.017][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.020][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.028][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.030][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.033][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.042][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.043][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.046][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.055][ef$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:50.057][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:50.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.060][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.062][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:50.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:50.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.069][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:29:50.071][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:29:50.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.074][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.076][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:29:50.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:29:50.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.082][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-12-21 16:29:50.084][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:29:50.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.087][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.089][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-12-21 16:29:50.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:29:50.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.115][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:29:50.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:29:50.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.121][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:29:50.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:29:50.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.128][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-12-21 16:29:50.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-12-21 16:29:50.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.134][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:29:50.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:29:50.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.140][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:29:50.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:29:50.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.146][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-12-21 16:29:50.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-12-21 16:29:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:29:50.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:29:50.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:29:50.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:29:50.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-12-21 16:29:50.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-12-21 16:29:50.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:50.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:50.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:50.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:50.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-12-21 16:29:50.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.192][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:50.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:50.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.198][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:50.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:50.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.204][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:50.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-12-21 16:29:50.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.211][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:50.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:50.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:50.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:50.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.271][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:50.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-12-21 16:29:50.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.278][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:29:50.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:29:50.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.285][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:29:50.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:29:50.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.291][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-12-21 16:29:50.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-12-21 16:29:50.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.297][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:50.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:50.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.303][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:50.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:50.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.310][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:50.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:50.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:29:50.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:29:50.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.375][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:29:50.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:29:50.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-12-21 16:29:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-12-21 16:29:50.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:29:50.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:29:50.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:29:50.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:29:50.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-12-21 16:29:50.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-12-21 16:29:50.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.500][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:50.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:50.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.506][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:50.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:50.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.513][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:50.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-12-21 16:29:50.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-12-21 16:29:50.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.568][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:50.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:50.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.575][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:50.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:50.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.601][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:50.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-12-21 16:29:50.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.609][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:50.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:50.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.616][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:50.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:50.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:50.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:50.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.629][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:29:50.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:29:50.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.636][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:29:50.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:29:50.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.676][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-12-21 16:29:50.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-12-21 16:29:50.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.683][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-12-21 16:29:50.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.859][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.869][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-12-21 16:29:50.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-12-21 16:29:50.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:50.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:50.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.919][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:29:50.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:29:50.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.928][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:29:50.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:29:50.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.962][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:29:50.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-12-21 16:29:50.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:50.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-12-21 16:29:50.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-12-21 16:29:50.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:50.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:50.999][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-12-21 16:29:51.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-12-21 16:29:51.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-12-21 16:29:51.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:51.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:51.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-12-21 16:29:51.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-12-21 16:29:51.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:51.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:51.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-12-21 16:29:51.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-12-21 16:29:51.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:51.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-21 16:29:51.026][biodb::testThat]
biodb.INFO [2024-12-21 16:29:51.027][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-12-21 16:29:51.028][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:29:51.029][biodb::testThat]
biodb.TRACE[2024-12-21 16:29:51.033][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:51.035][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:51.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:51.037][ef$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:51.041][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-12-21 16:29:51.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:51.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:51.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:51.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:51.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:51.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:51.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:51.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:51.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:51.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:51.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:51.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:51.099][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-12-21 16:29:51.101][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-12-21 16:29:51.102][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-12-21 16:29:51.103][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-12-21 16:29:51.105][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:51.107][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:51.109][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-12-21 16:29:51.111][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:51.112][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-12-21 16:29:51.114][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-12-21 16:29:52.188][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-12-21 16:29:52.190][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml, HMDB0000005.xml, HMDB0000008.xml, HMDB0000010.xml, HMDB0000011.xml
biodb.DEBUG[2024-12-21 16:29:52.420][private$doGetEntryIds] COUNT IDS = 217920
biodb.DEBUG[2024-12-21 16:29:52.496][private$doSearchForEntries] All IDs = [217920]: "HMDB0000001, HMDB0000002, HMDB0000005, HMDB0000008, HMDB0000010, HMDB0000011, HMDB0000012, HMDB0000014, HMDB0000015, HMDB0000016, ..."
biodb.DEBUG[2024-12-21 16:29:52.498][private$doSearchForEntries] Total number of IDs = 217920
biodb.TRACE[2024-12-21 16:29:52.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:52.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:52.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:52.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:52.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:52.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:52.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:52.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:52.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:52.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:52.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:52.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:52.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:52.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:52.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:52.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:52.523][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-12-21 16:29:52.525][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-12-21 16:29:52.526][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-12-21 16:29:52.546][ef$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:52.549][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:52.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:52.551][ef$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:52.553][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-12-21 16:29:52.571][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:52.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:52.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:52.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:52.576][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:52.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:52.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:52.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:52.582][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:52.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:52.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:52.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:52.594][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis or 1MH, belongs to the class of organic compounds known as histidine and derivatives. 1MH is also classified as a methylamino acid. Methylamino acids are primarily proteogenic amino acids (found in proteins) which have been methylated (in situ) on their side chains by various methyltransferase enzymes. Histidine can be methylated at either the N1 or N3 position of its imidazole ring, yielding the isomers 1-methylhistidine (1MH; also referred to as pi-methylhistidine) or 3-methylhistidine (3MH; tau-methylhistidine), respectively. There is considerable confusion with regard to the nomenclature of the methylated nitrogen atoms on the imidazole ring of histidine and other histidine-containing peptides such as anserine. In particular, older literature (mostly prior to the year 2000) designated anserine (Npi methylated) as beta-alanyl-N1-methyl-histidine, whereas according to standard IUPAC nomenclature, anserine is correctly named as beta-alanyl-N3-methyl-histidine. As a result, many papers published prior to the year 2000 incorrectly identified 1MH as a specific marker for dietary consumption or various pathophysiological effects when they really were referring to 3MH (PMID: 24137022).  Recent discoveries have shown that 1MH is produced in essentially all mammals (and other vertebrates) via the enzyme known as METTL9 (PMID: 33563959). METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mammalian proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where "x" is a small amino acid. This HxH motif is found in a number of abundant mammalian proteins such as ARMC6, S100A9, and NDUFB3 (PMID: 33563959). Because of its abundance in many muscle-related proteins, 1MH has been found to be a good biomarker for the consumption of meat (PMID: 21527577). Dietary studies have shown that poultry consumption (p-trend = 0.0006) and chicken consumption (p-trend = 0.0003) are associated with increased levels of 1MH in human plasma (PMID: 30018457). The consumption of fish, especially salmon and cod, has also been shown to increase the levels of 1MH in serum and urine (PMID: 31401679). As a general rule, urinary 1MH is associated with white meat intake (p< 0.001), whereas urinary 3MH is associated with red meat intake (p< 0.001) (PMID: 34091671).".
biodb.DEBUG[2024-12-21 16:29:52.674][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-12-21 16:29:52.675][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis or 1MH, belongs to the class of organic compounds known as histidine and derivatives. 1MH is also classified as a methylamino acid. Methylamino acids are primarily proteogenic amino acids (found in proteins) which have been methylated (in situ) on their side chains by various methyltransferase enzymes. Histidine can be methylated at either the N1 or N3 position of its imidazole ring, yielding the isomers 1-methylhistidine (1MH; also referred to as pi-methylhistidine) or 3-methylhistidine (3MH; tau-methylhistidine), respectively. There is considerable confusion with regard to the nomenclature of the methylated nitrogen atoms on the imidazole ring of histidine and other histidine-containing peptides such as anserine. In particular, older literature (mostly prior to the year 2000) designated anserine (Npi methylated) as beta-alanyl-N1-methyl-histidine, whereas according to standard IUPAC nomenclature, anserine is correctly named as beta-alanyl-N3-methyl-histidine. As a result, many papers published prior to the year 2000 incorrectly identified 1MH as a specific marker for dietary consumption or various pathophysiological effects when they really were referring to 3MH (PMID: 24137022).  Recent discoveries have shown that 1MH is produced in essentially all mammals (and other vertebrates) via the enzyme known as METTL9 (PMID: 33563959). METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mammalian proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where "x" is a small amino acid. This HxH motif is found in a number of abundant mammalian proteins such as ARMC6, S100A9, and NDUFB3 (PMID: 33563959). Because of its abundance in many muscle-related proteins, 1MH has been found to be a good biomarker for the consumption of meat (PMID: 21527577). Dietary studies have shown that poultry consumption (p-trend = 0.0006) and chicken consumption (p-trend = 0.0003) are associated with increased levels of 1MH in human plasma (PMID: 30018457). The consumption of fish, especially salmon and cod, has also been shown to increase the levels of 1MH in serum and urine (PMID: 31401679). As a general rule, urinary 1MH is associated with white meat intake (p< 0.001), whereas urinary 3MH is associated with red meat intake (p< 0.001) (PMID: 34091671).
biodb.DEBUG[2024-12-21 16:29:52.677][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis or 1MH, belongs to the class of organic compounds known as histidine and derivatives. 1MH is also classified as a methylamino acid. Methylamino acids are primarily proteogenic amino acids (found in proteins) which have been methylated (in situ) on their side chains by various methyltransferase enzymes. Histidine can be methylated at either the N1 or N3 position of its imidazole ring, yielding the isomers 1-methylhistidine (1MH; also referred to as pi-methylhistidine) or 3-methylhistidine (3MH; tau-methylhistidine), respectively. There is considerable confusion with regard to the nomenclature of the methylated nitrogen atoms on the imidazole ring of histidine and other histidine-containing peptides such as anserine. In particular, older literature (mostly prior to the year 2000) designated anserine (Npi methylated) as beta-alanyl-N1-methyl-histidine, whereas according to standard IUPAC nomenclature, anserine is correctly named as beta-alanyl-N3-methyl-histidine. As a result, many papers published prior to the year 2000 incorrectly identified 1MH as a specific marker for dietary consumption or various pathophysiological effects when they really were referring to 3MH (PMID: 24137022).  Recent discoveries have shown that 1MH is produced in essentially all mammals (and other vertebrates) via the enzyme known as METTL9 (PMID: 33563959). METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mammalian proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where "x" is a small amino acid. This HxH motif is found in a number of abundant mammalian proteins such as ARMC6, S100A9, and NDUFB3 (PMID: 33563959). Because of its abundance in many muscle-related proteins, 1MH has been found to be a good biomarker for the consumption of meat (PMID: 21527577). Dietary studies have shown that poultry consumption (p-trend = 0.0006) and chicken consumption (p-trend = 0.0003) are associated with increased levels of 1MH in human plasma (PMID: 30018457). The consumption of fish, especially salmon and cod, has also been shown to increase the levels of 1MH in serum and urine (PMID: 31401679). As a general rule, urinary 1MH is associated with white meat intake (p< 0.001), whereas urinary 3MH is associated with red meat intake (p< 0.001) (PMID: 34091671).
biodb.DEBUG[2024-12-21 16:29:52.697][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:52.699][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:52.701][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-12-21 16:29:52.702][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:52.704][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-12-21 16:29:52.726][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-12-21 16:29:53.828][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-12-21 16:29:53.829][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml, HMDB0000005.xml, HMDB0000008.xml, HMDB0000010.xml, HMDB0000011.xml
biodb.DEBUG[2024-12-21 16:29:54.058][private$doGetEntryIds] COUNT IDS = 217920
biodb.DEBUG[2024-12-21 16:29:54.136][private$doSearchForEntries] All IDs = [217920]: "HMDB0000001, HMDB0000002, HMDB0000005, HMDB0000008, HMDB0000010, HMDB0000011, HMDB0000012, HMDB0000014, HMDB0000015, HMDB0000016, ..."
biodb.DEBUG[2024-12-21 16:29:54.137][private$doSearchForEntries] Total number of IDs = 217920
biodb.TRACE[2024-12-21 16:29:54.140][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:54.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:54.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:54.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:54.145][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:54.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:54.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:54.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:54.150][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:54.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:54.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:54.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:54.155][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:29:54.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:29:54.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:54.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:54.160][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-12-21 16:29:54.162][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-12-21 16:29:54.163][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-12-21 16:29:54.182][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:54.183][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:54.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:54.186][ef$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:54.187][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-12-21 16:29:54.206][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:54.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:54.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:54.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:54.211][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:54.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:54.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:54.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:54.216][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:54.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:54.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:54.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:54.225][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-12-21 16:29:54.227][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-12-21 16:29:54.228][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-12-21 16:29:54.229][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-12-21 16:29:54.231][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:54.233][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:54.235][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-12-21 16:29:54.237][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:54.238][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-12-21 16:29:54.240][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-12-21 16:29:55.274][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-12-21 16:29:55.275][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml, HMDB0000005.xml, HMDB0000008.xml, HMDB0000010.xml, HMDB0000011.xml
biodb.DEBUG[2024-12-21 16:29:55.502][private$doGetEntryIds] COUNT IDS = 217920
biodb.DEBUG[2024-12-21 16:29:55.631][private$doSearchForEntries] All IDs = [217920]: "HMDB0000001, HMDB0000002, HMDB0000005, HMDB0000008, HMDB0000010, HMDB0000011, HMDB0000012, HMDB0000014, HMDB0000015, HMDB0000016, ..."
biodb.DEBUG[2024-12-21 16:29:55.632][private$doSearchForEntries] Total number of IDs = 217920
biodb.TRACE[2024-12-21 16:29:55.634][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:55.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:55.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:55.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:55.640][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:55.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:55.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:55.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:55.645][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:55.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:55.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:55.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:55.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:29:55.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:55.656][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-12-21 16:29:55.657][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-12-21 16:29:55.658][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-12-21 16:29:55.678][biodb::testThat]
biodb.INFO [2024-12-21 16:29:55.679][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-12-21 16:29:55.681][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:29:55.682][biodb::testThat]
biodb.TRACE[2024-12-21 16:29:55.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:55.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:55.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:55.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:55.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:55.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:55.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:55.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:55.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:55.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:55.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:55.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:55.730][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-12-21 16:29:55.732][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-12-21 16:29:55.733][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-12-21 16:29:55.735][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:55.737][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:55.738][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-12-21 16:29:55.740][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-12-21 16:29:55.741][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-12-21 16:29:55.743][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-12-21 16:29:56.754][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-12-21 16:29:56.755][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml, HMDB0000005.xml, HMDB0000008.xml, HMDB0000010.xml, HMDB0000011.xml
biodb.DEBUG[2024-12-21 16:29:56.978][private$doGetEntryIds] COUNT IDS = 217920
biodb.DEBUG[2024-12-21 16:29:57.145][private$doSearchForEntries] All IDs = [217920]: "HMDB0000001, HMDB0000002, HMDB0000005, HMDB0000008, HMDB0000010, HMDB0000011, HMDB0000012, HMDB0000014, HMDB0000015, HMDB0000016, ..."
biodb.DEBUG[2024-12-21 16:29:57.146][private$doSearchForEntries] Total number of IDs = 217920
biodb.TRACE[2024-12-21 16:29:57.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:57.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:57.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:57.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:57.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:57.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:57.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.163][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:29:57.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:29:57.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-12-21 16:29:57.168][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-12-21 16:29:57.169][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-12-21 16:29:57.190][biodb::testThat]
biodb.INFO [2024-12-21 16:29:57.191][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-12-21 16:29:57.192][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:29:57.193][biodb::testThat]
biodb.TRACE[2024-12-21 16:29:57.223][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-21 16:29:57.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-21 16:29:57.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.228][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-21 16:29:57.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-21 16:29:57.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.233][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-21 16:29:57.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-21 16:29:57.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.239][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-21 16:29:57.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-21 16:29:57.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.301][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-21 16:29:57.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-21 16:29:57.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.306][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-12-21 16:29:57.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-12-21 16:29:57.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.311][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-12-21 16:29:57.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-12-21 16:29:57.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:29:57.316][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-12-21 16:29:57.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-12-21 16:29:57.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:29:57.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-12-21 16:29:57.331][biodb::testThat]
biodb.INFO [2024-12-21 16:29:57.332][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-12-21 16:29:57.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:29:57.336][biodb::testThat]
biodb.INFO [2024-12-21 16:29:57.349][biodb::testThat]
biodb.INFO [2024-12-21 16:29:57.350][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-12-21 16:29:57.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:29:57.353][biodb::testThat]
biodb.INFO [2024-12-21 16:29:57.365][biodb::testThat]
biodb.INFO [2024-12-21 16:29:57.366][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-12-21 16:29:57.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:29:57.369][biodb::testThat]
biodb.DEBUG[2024-12-21 16:29:57.374][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-12-21 16:30:06.229][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-12-21 16:30:06.341][biodb::testThat]
biodb.INFO [2024-12-21 16:30:06.342][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-12-21 16:30:06.344][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-12-21 16:30:06.345][biodb::testThat]
biodb.DEBUG[2024-12-21 16:30:06.668][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-12-21 16:30:06.772][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:30:06.774][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:30:06.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:30:06.776][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:30:06.777][ef$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:30:06.779][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:30:06.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:30:06.781][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:30:06.782][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:30:06.784][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:30:06.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:30:06.786][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:30:06.787][ef$get] Asked field names are: name.
biodb.TRACE[2024-12-21 16:30:06.789][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-12-21 16:30:06.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:30:06.791][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:30:06.792][ef$get] Asked field names are: description.
biodb.TRACE[2024-12-21 16:30:06.794][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-12-21 16:30:06.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:30:06.796][ef$get] fields variable is a list.
biodb.TRACE[2024-12-21 16:30:06.798][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-12-21 16:30:06.799][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-12-21 16:30:06.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-12-21 16:30:06.802][ef$get] fields variable is a list.
biodb.INFO [2024-12-21 16:30:06.804][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-12-21 16:30:06.805][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-12-21 16:30:06.807][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-12-21 16:30:06.809][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-12-21 16:30:06.810][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-12-21 16:30:06.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-12-21 16:30:06.813][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-12-21 16:30:06.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-12-21 16:30:06.816][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-12-21 16:30:06.817][FUN] Functions in observer 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 
1028.506  192.291 1647.425

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)