Back to Long Tests report for BioC 3.20

This page was generated on 2024-06-15 23:55 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4420
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
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 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-15 09:55 -0400 (Sat, 15 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: c3d59a4
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  WARNINGS  
palomino4Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on palomino4

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: 1.11.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.11.0.tar.gz
StartedAt: 2024-06-15 16:16:03 -0400 (Sat, 15 Jun 2024)
EndedAt: 2024-06-15 20:58:12 -0400 (Sat, 15 Jun 2024)
EllapsedTime: 16928.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-06-15 16:23:18.989][biodb::testContext]
biodb.INFO [2024-06-15 16:23:19.001][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-15 16:23:19.002][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-15 16:23:19.004][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-15 16:23:19.005][biodb::testContext]
biodb.INFO [2024-06-15 16:23:19.012][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-15 16:23:19.017][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-15 16:23:19.031][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:23:19.033][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-15 16:23:19.035][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-15 16:23:19.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.042][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-15 16:23:19.061][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-15 16:23:19.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.068][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-15 16:23:19.070][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-15 16:23:19.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.075][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-15 16:23:19.076][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-15 16:23:19.078][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-15 16:23:19.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.082][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[2024-06-15 16:23:19.083][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-15 16:23:19.084][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-15 16:23:19.086][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-15 16:23:19.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.092][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-15 16:23:19.093][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-15 16:23:19.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.098][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-15 16:23:19.100][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-15 16:23:19.101][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-15 16:23:19.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.106][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-15 16:23:19.107][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-15 16:23:19.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.111][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-15 16:23:19.113][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-15 16:23:19.115][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-15 16:23:19.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.120][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-15 16:23:19.121][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-15 16:23:19.122][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-15 16:23:19.124][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-15 16:23:19.125][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-15 16:23:19.127][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-15 16:23:19.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.133][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-15 16:23:19.134][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-15 16:23:19.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.138][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-15 16:23:19.140][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-15 16:23:19.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.145][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-15 16:23:19.146][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-15 16:23:19.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.151][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-15 16:23:19.152][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-15 16:23:19.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.157][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-15 16:23:19.158][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-15 16:23:19.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.165][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-15 16:23:19.167][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-15 16:23:19.171][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-15 16:23:19.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.175][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-15 16:23:19.177][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-15 16:23:19.178][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-15 16:23:19.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.186][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-15 16:23:19.241][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.256][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-15 16:23:19.258][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.260][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:23:19.261][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.262][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.263][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.265][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.266][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-15 16:23:19.267][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:23:19.268][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.270][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-15 16:23:19.271][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:23:19.272][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.273][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.274][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:23:19.274][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-15 16:23:19.274][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-15 16:23:19.274][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-15 16:23:19.274][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-15 16:23:19.276][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:23:19.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.279][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:23:19.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.283][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.284][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.285][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:23:19.287][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:23:19.288][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.289][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.291][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-15 16:23:19.293][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.294][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-15 16:23:19.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:23:19.298][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.299][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.301][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.302][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.303][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-15 16:23:19.304][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:23:19.306][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.307][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-15 16:23:19.308][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:23:19.310][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.311][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.312][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:23:19.312][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-15 16:23:19.312][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-15 16:23:19.312][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-15 16:23:19.312][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-15 16:23:19.314][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:23:19.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.317][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:23:19.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.321][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.322][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.323][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:23:19.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:23:19.325][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.327][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.328][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-15 16:23:19.330][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.331][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-15 16:23:19.332][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.334][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:23:19.335][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.336][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.337][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.338][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.340][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-15 16:23:19.341][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:23:19.342][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.343][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-15 16:23:19.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:23:19.347][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.349][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.351][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.352][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:23:19.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.357][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:23:19.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.363][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.365][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:23:19.366][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:23:19.367][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.368][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.370][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-15 16:23:19.372][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.373][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-15 16:23:19.374][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.376][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:23:19.377][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.378][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.379][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.381][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.382][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-15 16:23:19.383][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:23:19.385][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.387][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-15 16:23:19.388][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:23:19.389][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.391][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.392][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.393][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:23:19.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.397][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:23:19.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.399][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.400][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.402][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.403][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:23:19.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:23:19.405][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.406][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:19.410][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:23:19.411][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.519][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-15 16:23:19.522][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-15 16:23:19.524][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-15 16:23:19.526][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-15 16:23:19.527][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-15 16:23:19.529][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-15 16:23:19.532][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-15 16:23:19.534][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-15 16:23:19.536][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-15 16:23:19.537][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-15 16:23:19.539][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-15 16:23:19.541][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-15 16:23:19.543][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-15 16:23:19.544][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-15 16:23:19.546][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-15 16:23:19.548][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-15 16:23:19.549][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-15 16:23:19.551][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-15 16:23:19.552][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-15 16:23:19.554][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-15 16:23:19.556][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-15 16:23:19.557][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-15 16:23:19.560][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-15 16:23:19.561][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-15 16:23:19.563][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-15 16:23:19.565][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-15 16:23:19.566][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-15 16:23:19.568][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-15 16:23:19.570][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-15 16:23:19.572][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-15 16:23:19.573][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-15 16:23:19.575][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-15 16:23:19.577][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-15 16:23:19.579][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-15 16:23:19.582][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-15 16:23:19.584][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-15 16:23:19.586][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-15 16:23:19.588][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-15 16:23:19.591][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-15 16:23:19.593][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-15 16:23:19.595][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-15 16:23:19.597][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-15 16:23:19.600][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-15 16:23:19.602][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-15 16:23:19.604][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-15 16:23:19.606][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-15 16:23:19.608][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-15 16:23:19.611][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-15 16:23:19.613][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-15 16:23:19.615][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-15 16:23:19.617][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-15 16:23:19.620][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-15 16:23:19.622][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-15 16:23:19.624][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-15 16:23:19.625][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-15 16:23:19.627][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-15 16:23:19.628][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-15 16:23:19.631][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-15 16:23:19.633][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-15 16:23:19.634][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-15 16:23:19.636][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-15 16:23:19.638][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-15 16:23:19.639][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-15 16:23:19.641][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-15 16:23:19.642][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-15 16:23:19.644][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-15 16:23:19.645][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-15 16:23:19.647][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-15 16:23:19.649][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-15 16:23:19.650][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-15 16:23:19.652][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-15 16:23:19.653][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-15 16:23:19.655][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-15 16:23:19.656][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-15 16:23:19.658][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-15 16:23:19.660][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-15 16:23:19.661][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-15 16:23:19.663][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-15 16:23:19.664][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-15 16:23:19.666][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-15 16:23:19.667][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-15 16:23:19.669][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-15 16:23:19.670][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-15 16:23:19.719][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-15 16:23:19.723][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-15 16:23:19.726][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:23:19.727][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.729][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.901][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-15 16:23:19.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:23:19.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:19.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:19.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:19.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:19.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:19.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:23:19.918][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-06-15 16:23:19.935][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-06-15 16:23:19.939][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.941][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.943][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.945][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:23:19.947][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.948][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-06-15 16:23:19.950][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.951][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.953][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-15 16:23:19.954][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:23:19.956][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.957][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-06-15 16:23:19.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-06-15 16:23:19.960][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-06-15 16:23:19.961][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-15 16:23:19.962][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:23:19.962][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-06-15 16:23:19.962][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-06-15 16:23:19.964][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-15 16:23:19.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.967][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:23:19.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:23:19.970][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:23:19.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:23:19.972][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-06-15 16:23:19.972][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-06-15 16:23:19.973][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:23:19.975][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:23:19.976][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-15 16:23:19.977][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:23:20.020][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-06-15 16:23:20.023][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-15 16:23:20.026][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-15 16:23:20.029][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-15 16:23:20.033][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-15 16:23:20.070][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-06-15 16:23:20.072][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-06-15 16:23:20.078][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-06-15 16:23:20.083][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-06-15 16:23:20.088][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-15 16:23:20.089][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-15 16:23:20.091][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-06-15 16:23:20.093][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-06-15 16:23:20.110][biodb::testThat]
biodb.INFO [2024-06-15 16:23:20.112][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-15 16:23:20.114][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:23:20.115][biodb::testThat]
biodb.TRACE[2024-06-15 16:23:20.122][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-06-15 16:23:20.124][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-15 16:23:20.129][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-15 16:23:20.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-15 16:23:20.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:23:20.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:23:20.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:23:20.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:23:20.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:23:20.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-15 16:23:20.210][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:20.212][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:20.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.216][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:20.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:20.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.248][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.251][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.256][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.297][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.307][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.309][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.313][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.316][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.324][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.326][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.330][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.332][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.340][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.342][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.345][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.355][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.357][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.361][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.389][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.391][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.395][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.397][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.405][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.407][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.411][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.414][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.421][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.422][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.424][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.426][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.434][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.436][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.440][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.447][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:20.448][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:20.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.450][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.452][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:20.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:20.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.457][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:20.458][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:20.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.461][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:20.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:20.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.467][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.469][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.481][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.483][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.487][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.496][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.502][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.509][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:20.510][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:20.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.513][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.514][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:20.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:20.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.520][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:20.521][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:20.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.523][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.525][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:20.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:20.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.530][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-06-15 16:23:20.532][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:20.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.534][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.536][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-06-15 16:23:20.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:20.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:20.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:20.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:20.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:20.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:20.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:20.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.604][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.612][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.619][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:20.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.627][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.634][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.640][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:20.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:20.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:20.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.689][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.703][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:20.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.708][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.713][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:20.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.723][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:20.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:20.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.730][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:20.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:20.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.737][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:20.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:20.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.742][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:20.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:20.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.747][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:20.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:20.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.752][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:20.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:20.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:20.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:20.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:20.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:20.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:20.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:20.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:20.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:20.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:20.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:20.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.801][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.811][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.816][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:20.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.841][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.851][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.856][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.861][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:20.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.866][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.871][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.876][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:20.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.881][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:20.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:20.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.886][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:20.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:20.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:20.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:20.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.896][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-15 16:23:20.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.915][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-06-15 16:23:20.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:20.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:20.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:20.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.961][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:20.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:20.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.966][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:20.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:20.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:20.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:20.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.976][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:20.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:20.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:20.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:20.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:20.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:20.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:20.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:20.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-15 16:23:21.025][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-06-15 16:23:21.030][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:23:21.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:23:21.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.037][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:23:21.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:23:21.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.044][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-15 16:23:21.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-15 16:23:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.052][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-15 16:23:21.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-15 16:23:21.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.400][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:21.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:21.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.463][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:21.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:21.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.470][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:21.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:21.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.477][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:21.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 16:23:21.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.522][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.524][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.527][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:21.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:21.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.560][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.568][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.575][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.582][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.584][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.587][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.589][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:21.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.633][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.635][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.639][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:21.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.662][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.670][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.677][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.684][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.686][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.689][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.691][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:21.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.735][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.737][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.740][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:21.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.761][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.766][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.771][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.777][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.778][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.781][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.782][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:21.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:21.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:21.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:21.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:21.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:21.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:21.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.823][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:21.825][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:21.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.828][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:21.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:21.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.851][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:21.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:21.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.858][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:21.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:21.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.866][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:21.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:21.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.874][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:21.875][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:21.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.881][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:21.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:21.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:21.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:21.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.910][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:21.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:21.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.917][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:21.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:21.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.924][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:21.926][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:21.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.929][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.931][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:21.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:21.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.951][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.960][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.965][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.970][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.971][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.975][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:21.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:21.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:21.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:21.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:21.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:21.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:21.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:22.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:22.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.005][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:22.007][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:22.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.009][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:22.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:22.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.026][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.031][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.047][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.048][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.051][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.052][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.074][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.081][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.096][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.098][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.103][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.124][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.132][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.139][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.146][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.148][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.152][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.153][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.176][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:22.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:22.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.184][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:22.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:22.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.191][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:22.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:22.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.198][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:22.200][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:22.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:22.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:22.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:22.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:22.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:22.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:22.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:22.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:22.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.241][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:22.242][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:22.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.245][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:22.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:22.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.290][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.292][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.319][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.327][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.334][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.342][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.343][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.347][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.349][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.371][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:23:22.373][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:23:22.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.377][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.393][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-15 16:23:22.395][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-15 16:23:22.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.399][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.410][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.412][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-15 16:23:22.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.416][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.426][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-15 16:23:22.428][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-15 16:23:22.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.432][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.442][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:22.444][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-06-15 16:23:22.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.455][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.457][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-06-15 16:23:22.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.459][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.466][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.468][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-06-15 16:23:22.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.470][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.478][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.479][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-06-15 16:23:22.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.482][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.489][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-15 16:23:22.490][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 16:23:22.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.493][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.505][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-15 16:23:22.507][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-15 16:23:22.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.510][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.521][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-15 16:23:22.523][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-15 16:23:22.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.526][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.536][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.539][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-15 16:23:22.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.542][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.553][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:22.555][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-15 16:23:22.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.559][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:22.571][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-15 16:23:22.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.575][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.594][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:23:22.596][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:23:22.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.599][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.610][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:22.612][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-06-15 16:23:22.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.615][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.626][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:22.628][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 16:23:22.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.632][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:23:22.642][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-15 16:23:22.644][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-15 16:23:22.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:23:22.648][ef$get] fields variable is a list.
biodb.INFO [2024-06-15 16:23:22.666][biodb::testThat]
biodb.INFO [2024-06-15 16:23:22.668][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-15 16:23:22.670][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:23:22.672][biodb::testThat]
biodb.DEBUG[2024-06-15 16:23:22.693][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-06-15 16:23:22.703][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-06-15 16:23:22.714][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-06-15 16:23:22.718][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-06-15 16:23:22.720][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-06-15 16:23:22.722][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-06-15 16:23:22.726][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[2024-06-15 16:23:30.408][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\hmdb.metabolites21b38127d6c0zip".
biodb.TRACE[2024-06-15 16:23:30.411][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-15 16:23:30.491][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-15 16:23:30.495][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-15 16:23:30.497][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-06-15 16:23:30.501][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker21b38b2e1831marker".
biodb.TRACE[2024-06-15 16:23:30.503][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-06-15 16:23:30.509][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-15 16:23:30.512][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-06-15 16:23:30.515][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-06-15 16:23:30.517][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-06-15 16:23:30.520][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-06-15 16:23:30.522][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp...
biodb.DEBUG[2024-06-15 16:24:09.344][private$findXmlDatabaseFile] Found files [1]: "hmdb_metabolites.xml" into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-06-15 16:24:09.347][private$findXmlDatabaseFile] Found XML file C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml in ZIP file.
biodb.DEBUG[2024-06-15 16:24:09.349][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-06-15 16:24:09.352][private$doExtractDownload] Extract entries from XML file "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml", into "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp".
biodb.TRACE[2024-06-15 16:43:55.140][self$addFilesToCache] Moving files to cache [217920]: "C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000016.xml, ...".
biodb.TRACE[2024-06-15 16:43:56.177][private$doAddFilesToCache] Destination files are [217920]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000016.xml, ...".
biodb.DEBUG[2024-06-15 20:57:46.872][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-15 20:57:46.876][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-06-15 20:57:46.886][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker21b3828757f33marker".
biodb.TRACE[2024-06-15 20:57:46.887][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-06-15 20:57:46.893][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-06-15 20:57:46.895][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-06-15 20:57:46.897][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-15 20:57:46.898][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-15 20:57:46.900][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-06-15 20:57:46.902][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-06-15 20:57:46.931][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-06-15 20:57:46.933][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-06-15 20:57:46.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-15 20:57:46.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 20:57:46.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 20:57:46.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 20:57:46.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 20:57:46.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-15 20:57:46.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-15 20:57:46.965][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 20:57:46.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 20:57:46.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:46.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:46.970][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 20:57:46.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-06-15 20:57:46.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:46.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:46.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 20:57:46.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 20:57:46.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:46.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:46.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 20:57:46.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 20:57:46.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:46.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:46.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 20:57:46.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 20:57:46.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:46.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:46.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 20:57:46.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 20:57:46.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:46.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:47.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 20:57:47.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 20:57:47.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:47.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:47.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 20:57:47.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 20:57:47.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:47.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-15 20:57:47.013][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-06-15 20:57:47.014][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-15 20:57:47.116][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.118][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-15 20:57:47.119][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 20:57:47.120][biodb::testThat]
biodb.TRACE[2024-06-15 20:57:47.124][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 20:57:47.125][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 20:57:47.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:47.127][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-15 20:57:47.130][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.INFO [2024-06-15 20:57:47.552][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.554][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-15 20:57:47.555][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 20:57:47.556][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.693][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.694][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-15 20:57:47.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 20:57:47.697][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.840][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.841][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-15 20:57:47.843][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 20:57:47.844][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.856][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.857][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-15 20:57:47.858][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 20:57:47.859][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.871][biodb::testThat]
biodb.INFO [2024-06-15 20:57:47.872][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-15 20:57:47.873][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 20:57:47.875][biodb::testThat]
biodb.DEBUG[2024-06-15 20:57:47.879][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-06-15 20:57:48.521][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-06-15 20:57:49.355][biodb::testThat]
biodb.INFO [2024-06-15 20:57:49.356][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-15 20:57:49.358][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 20:57:49.359][biodb::testThat]
biodb.DEBUG[2024-06-15 20:57:49.498][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-06-15 20:57:49.647][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 20:57:49.649][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 20:57:49.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:49.651][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:49.653][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-15 20:57:49.654][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 20:57:49.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:49.657][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:49.658][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 20:57:49.659][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 20:57:49.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:49.662][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:49.663][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 20:57:49.665][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 20:57:49.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:49.667][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:49.668][ef$get] Asked field names are: description.
biodb.TRACE[2024-06-15 20:57:49.670][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-06-15 20:57:49.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:49.672][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 20:57:49.674][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-06-15 20:57:49.675][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-06-15 20:57:49.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 20:57:49.677][ef$get] fields variable is a list.
biodb.INFO [2024-06-15 20:57:49.679][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-15 20:57:49.680][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-06-15 20:57:49.683][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-06-15 20:57:49.685][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-15 20:57:49.686][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 20:57:49.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 20:57:49.688][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 20:57:49.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 20:57:49.691][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 20:57:49.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 7 | WARN 217255 | SKIP 0 | PASS 115 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
── Failure ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
── Failure ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")

[ FAIL 7 | WARN 217255 | SKIP 0 | PASS 115 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.11.0'
* 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 whether package 'biodbHmdb' can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
  ── Failure ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
  `e` inherits from `'NULL'` not `'character'`.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─testthat::expect_is(e, "BiodbEntry")
  
  [ FAIL 7 | WARN 217255 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log'
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package 'biodbHmdb' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor 'EntryMaker::EntryMaker()':
EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbHmdb.dll tmp.def 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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)