Back to Long Tests report for BioC 3.19

This page was generated on 2024-10-12 23:55 -0400 (Sat, 12 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4529
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/33HostnameOS / ArchCHECK
biodbExpasy 1.8.1  (landing page)
Pierrick Roger
Snapshot Date: 2024-10-12 09:55 -0400 (Sat, 12 Oct 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_19
git_last_commit: 8918846
git_last_commit_date: 2024-08-03 12:10:16 -0400 (Sat, 03 Aug 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on nebbiolo1

To the developers/maintainers of the biodbExpasy 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: biodbExpasy
Version: 1.8.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.1.tar.gz
StartedAt: 2024-10-12 16:04:03 -0400 (Sat, 12 Oct 2024)
EndedAt: 2024-10-12 16:04:48 -0400 (Sat, 12 Oct 2024)
EllapsedTime: 45.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-10-12 16:04:40.029][biodb::testContext]
biodb.INFO [2024-10-12 16:04:40.031][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:04:40.032][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-10-12 16:04:40.033][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:04:40.034][biodb::testContext]
biodb.INFO [2024-10-12 16:04:40.041][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:04:40.043][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:04:40.051][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:40.052][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:04:40.053][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:04:40.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.057][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:04:40.076][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:04:40.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.080][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:04:40.081][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:04:40.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.085][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:04:40.086][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:04:40.087][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:04:40.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.091][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:04:40.092][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:04:40.093][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:04:40.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.097][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:04:40.098][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:04:40.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.101][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:04:40.102][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:04:40.103][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:04:40.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.107][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:04:40.108][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:04:40.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.112][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:04:40.113][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:04:40.114][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:04:40.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.118][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:04:40.119][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:04:40.120][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:04:40.121][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:04:40.122][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:04:40.123][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:04:40.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.127][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:04:40.128][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:04:40.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.131][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:04:40.132][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:04:40.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.136][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:04:40.137][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:04:40.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.141][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:04:40.142][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:04:40.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.146][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:04:40.147][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:04:40.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.150][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:04:40.151][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:04:40.156][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:04:40.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.160][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:04:40.161][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:04:40.162][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:04:40.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.169][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:04:40.204][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.227][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-12 16:04:40.228][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.229][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:40.230][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.230][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.231][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.232][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.233][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:04:40.234][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:40.235][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.236][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:04:40.237][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:40.238][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.238][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.239][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:40.239][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:04:40.239][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:04:40.239][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:04:40.239][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:04:40.240][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:40.241][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.242][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.243][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:40.244][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.244][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.245][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.246][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.247][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:40.248][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:40.249][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.249][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.251][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:04:40.252][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.253][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:04:40.254][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.255][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:40.256][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.257][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.257][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.258][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.259][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:04:40.260][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:40.261][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.262][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:04:40.263][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:40.264][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.265][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.265][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:40.265][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:04:40.265][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:04:40.265][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:04:40.265][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:04:40.266][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:40.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.269][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:40.270][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.271][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.272][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.273][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:40.274][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:40.275][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.276][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.277][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:04:40.278][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.279][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-12 16:04:40.280][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.281][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:40.282][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.283][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.284][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.285][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.285][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:04:40.286][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:40.287][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.288][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:04:40.289][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:40.290][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.291][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.292][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.293][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:40.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.295][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:40.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.298][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.298][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.299][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:40.300][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:40.301][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.302][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.303][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:04:40.304][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.305][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:04:40.306][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.307][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:40.308][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.309][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.310][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.311][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:04:40.312][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:40.313][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.314][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:04:40.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:40.316][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.317][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.318][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.319][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:40.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.320][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:40.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.324][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.324][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.325][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:40.326][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:40.327][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.328][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.332][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:40.332][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.411][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:04:40.417][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:04:40.418][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:04:40.419][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:04:40.421][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:04:40.422][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:04:40.424][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:04:40.425][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:04:40.426][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:04:40.428][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:04:40.429][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:04:40.430][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:04:40.432][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:04:40.433][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:04:40.434][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:04:40.436][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:04:40.437][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:04:40.439][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:04:40.440][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:04:40.441][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:04:40.443][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:04:40.444][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:04:40.445][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:04:40.447][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:04:40.448][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:04:40.449][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:04:40.451][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:04:40.452][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:04:40.454][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:04:40.455][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:04:40.456][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:04:40.458][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:04:40.459][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:04:40.460][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:04:40.462][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:04:40.463][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:04:40.464][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:04:40.466][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:04:40.467][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:04:40.468][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:04:40.470][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:04:40.471][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:04:40.473][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:04:40.474][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:04:40.488][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:04:40.489][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:04:40.490][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:04:40.492][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:04:40.493][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:04:40.494][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:04:40.496][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:04:40.497][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:04:40.498][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:04:40.500][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:04:40.501][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:04:40.502][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:04:40.504][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:04:40.505][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:04:40.507][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:04:40.508][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:04:40.509][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:04:40.511][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:04:40.512][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:04:40.514][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:04:40.515][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:04:40.516][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:04:40.518][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:04:40.519][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:04:40.520][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:04:40.522][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:04:40.523][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:04:40.525][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:04:40.526][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:04:40.527][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:04:40.529][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:04:40.530][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:04:40.531][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:04:40.533][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:04:40.534][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:04:40.535][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:04:40.537][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:04:40.538][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:04:40.539][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:04:40.545][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:04:40.547][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:04:40.550][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:40.551][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.553][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:40.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:40.658][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-10-12 16:04:40.667][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:04:40.668][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.669][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-10-12 16:04:40.670][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.671][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:40.672][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.673][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.674][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.675][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.676][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-10-12 16:04:40.676][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:40.677][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.678][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-10-12 16:04:40.679][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:40.680][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-10-12 16:04:40.680][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:04:40.680][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:04:40.680][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:04:40.681][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:40.682][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:40.683][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:04:40.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:40.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:40.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:40.688][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:40.689][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:04:40.690][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:40.690][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:40.691][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:40.692][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:40.697][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:04:40.719][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:04:40.720][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-10-12 16:04:40.725][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:04:40.729][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-10-12 16:04:40.733][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:04:40.734][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:04:40.740][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-10-12 16:04:40.749][biodb::testThat]
biodb.INFO [2024-10-12 16:04:40.750][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-12 16:04:40.751][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:40.751][biodb::testThat]
biodb.TRACE[2024-10-12 16:04:40.755][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-10-12 16:04:40.756][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:04:40.760][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:04:40.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:40.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:40.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:40.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:40.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:40.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:40.783][FUN] Functions in observer BiodbConfig: [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[2024-10-12 16:04:40.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.818][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:40.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:40.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.832][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:40.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:40.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.840][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:04:40.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.843][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.847][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.850][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.854][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:04:40.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:40.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:40.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:40.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:40.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:40.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:40.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:40.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:40.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:40.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:40.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:40.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.919][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:40.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:40.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.923][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:40.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:40.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.930][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:40.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:40.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:40.962][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-10-12 16:04:40.964][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:40.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:40.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.968][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:40.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:40.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.971][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:40.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:40.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.975][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:40.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:40.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:40.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:40.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:40.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:40.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.006][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.035][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.039][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.042][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.062][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.063][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.065][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.086][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.087][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.089][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.100][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.103][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.107][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.110][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.111][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.114][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.123][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.127][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.130][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.134][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.135][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.137][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.138][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.147][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.148][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.150][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.153][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.154][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.156][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.180][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.181][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.182][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.186][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.189][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.203][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-10-12 16:04:41.234][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-10-12 16:04:41.235][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:04:41.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:41.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:41.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:41.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:41.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:41.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:41.245][FUN] Functions in observer BiodbConfig: [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[2024-10-12 16:04:41.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.250][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.258][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:04:41.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:41.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.265][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.272][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:41.298][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-10-12 16:04:41.316][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:41.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:41.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.319][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:41.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:41.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.323][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:41.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:41.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.326][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:41.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:41.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.337][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.374][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.377][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:41.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.405][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.406][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.408][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.419][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.429][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.430][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.432][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.442][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.446][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.450][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.453][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.454][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.456][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.457][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.466][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:41.467][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:41.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.469][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.473][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.474][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:41.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.475][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:41.479][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:41.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:41.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:41.482][ef$get] fields variable is a list.
biodb.INFO [2024-10-12 16:04:41.488][biodb::testThat]
biodb.INFO [2024-10-12 16:04:41.489][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-12 16:04:41.490][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:41.490][biodb::testThat]
biodb.DEBUG[2024-10-12 16:04:41.492][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-10-12 16:04:41.499][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-10-12 16:04:41.503][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.TRACE[2024-10-12 16:04:41.505][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-10-12 16:04:41.506][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt".
biodb.DEBUG[2024-10-12 16:04:41.507][conn$getEntryContent] 1 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-10-12 16:04:41.508][conn$getEntryContent] 1 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:04:41.509][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-12 16:04:41.510][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-12 16:04:41.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:41.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:41.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:41.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:41.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:41.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:41.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:41.523][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-10-12 16:04:41.542][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-12 16:04:41.543][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-12 16:04:41.544][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-10-12 16:04:42.325][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-10-12 16:04:42.867][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-12 16:04:42.871][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-10-12 16:04:42.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-10-12 16:04:42.907][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-10-12 16:04:42.910][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-12 16:04:42.912][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-10-12 16:04:42.914][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-10-12 16:04:42.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:42.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:42.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:42.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:42.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:42.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:42.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:04:42.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:42.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:42.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.938][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:42.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:42.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:42.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:42.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.947][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:04:42.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:42.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:42.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:42.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:42.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:42.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:42.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:42.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:42.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:42.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:42.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:42.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.970][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:42.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:42.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.974][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:42.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:42.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:42.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:42.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.981][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:42.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:42.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:42.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:42.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:42.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:42.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:42.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:42.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:42.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:42.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:42.996][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-12 16:04:42.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:42.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:43.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:43.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:43.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:43.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-12 16:04:43.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.018][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:43.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-10-12 16:04:43.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:43.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:43.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.026][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-10-12 16:04:43.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-10-12 16:04:43.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.030][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:43.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:43.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.033][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:43.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:43.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.040][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:43.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-10-12 16:04:43.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-12 16:04:43.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-12 16:04:43.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:43.076][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-10-12 16:04:43.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:04:43.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:04:43.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:04:43.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:04:43.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:04:43.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:04:43.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-12 16:04:43.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-12 16:04:43.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:04:43.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-12 16:04:43.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:04:43.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-12 16:04:43.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:04:43.107][biodb::testThat]
biodb.INFO [2024-10-12 16:04:43.108][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-12 16:04:43.109][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:43.110][biodb::testThat]
biodb.TRACE[2024-10-12 16:04:43.113][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:43.114][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:43.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.115][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:43.116][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-10-12 16:04:43.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:43.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:43.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:43.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:43.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:43.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:43.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:43.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:43.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:43.150][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:04:43.170][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:04:43.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-12 16:04:43.188][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-12 16:04:43.201][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-10-12 16:04:43.820][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-10-12 16:04:44.551][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-12 16:04:44.555][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-10-12 16:04:44.563][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-10-12 16:04:44.575][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-10-12 16:04:44.601][biodb::testThat]
biodb.INFO [2024-10-12 16:04:44.603][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-12 16:04:44.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:44.606][biodb::testThat]
biodb.TRACE[2024-10-12 16:04:44.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:44.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:44.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:44.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:44.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:44.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:44.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-12 16:04:44.679][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-10-12 16:04:44.682][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-12 16:04:44.698][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-10-12 16:04:44.699][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-12 16:04:44.700][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-10-12 16:04:44.715][biodb::testThat]
biodb.INFO [2024-10-12 16:04:44.716][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-12 16:04:44.717][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:44.718][biodb::testThat]
biodb.TRACE[2024-10-12 16:04:44.727][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:44.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:44.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.731][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:44.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:44.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.735][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:44.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:44.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.739][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:44.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:44.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:44.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:44.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-12 16:04:44.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-12 16:04:44.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:44.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-12 16:04:44.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:44.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:44.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-12 16:04:44.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:44.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-12 16:04:44.810][biodb::testThat]
biodb.INFO [2024-10-12 16:04:44.810][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-12 16:04:44.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:44.812][biodb::testThat]
biodb.INFO [2024-10-12 16:04:44.820][biodb::testThat]
biodb.INFO [2024-10-12 16:04:44.821][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-12 16:04:44.822][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:44.823][biodb::testThat]
biodb.INFO [2024-10-12 16:04:44.830][biodb::testThat]
biodb.INFO [2024-10-12 16:04:44.831][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-12 16:04:44.831][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:44.832][biodb::testThat]
biodb.DEBUG[2024-10-12 16:04:44.844][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-10-12 16:04:45.366][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-10-12 16:04:46.112][biodb::testThat]
biodb.INFO [2024-10-12 16:04:46.115][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-12 16:04:46.117][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-12 16:04:46.119][biodb::testThat]
biodb.DEBUG[2024-10-12 16:04:46.591][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-10-12 16:04:47.240][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:47.243][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:47.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:47.247][ef$get] fields variable is a list.
biodb.TRACE[2024-10-12 16:04:47.249][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-12 16:04:47.251][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-12 16:04:47.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-12 16:04:47.254][ef$get] fields variable is a list.
biodb.INFO [2024-10-12 16:04:47.256][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:04:47.258][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-10-12 16:04:47.259][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-10-12 16:04:47.261][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:04:47.262][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.264][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.267][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-12 16:04:47.280][biodb::testContext]
biodb.INFO [2024-10-12 16:04:47.281][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:04:47.282][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-10-12 16:04:47.283][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-12 16:04:47.284][biodb::testContext]
biodb.INFO [2024-10-12 16:04:47.286][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:04:47.288][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-12 16:04:47.292][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:47.293][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-12 16:04:47.294][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-12 16:04:47.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.297][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-12 16:04:47.298][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-12 16:04:47.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.310][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-12 16:04:47.311][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-12 16:04:47.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.314][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-12 16:04:47.315][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-12 16:04:47.316][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-12 16:04:47.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.319][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-12 16:04:47.320][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-12 16:04:47.321][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-12 16:04:47.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.324][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-12 16:04:47.325][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-12 16:04:47.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.328][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-12 16:04:47.329][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-12 16:04:47.330][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-12 16:04:47.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.333][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-12 16:04:47.334][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-12 16:04:47.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.338][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-12 16:04:47.339][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-12 16:04:47.340][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-12 16:04:47.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.343][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:04:47.344][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-12 16:04:47.345][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-12 16:04:47.345][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-12 16:04:47.346][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-12 16:04:47.347][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-12 16:04:47.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.351][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-12 16:04:47.351][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-12 16:04:47.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.355][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-12 16:04:47.356][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-12 16:04:47.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.359][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-12 16:04:47.360][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-12 16:04:47.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.363][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-12 16:04:47.364][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-12 16:04:47.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.367][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-12 16:04:47.368][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-12 16:04:47.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.372][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-12 16:04:47.372][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-12 16:04:47.375][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-12 16:04:47.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.379][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-12 16:04:47.380][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-12 16:04:47.381][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-12 16:04:47.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.384][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-12 16:04:47.386][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.387][self$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[2024-10-12 16:04:47.387][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.388][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:47.389][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.390][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.391][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.392][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.393][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:04:47.394][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:47.395][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.396][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-12 16:04:47.396][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:47.397][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.398][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.399][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:47.399][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:04:47.399][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:04:47.399][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:04:47.399][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:04:47.400][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:47.401][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.402][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.403][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:47.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.405][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.406][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.407][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:47.408][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:47.409][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.409][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.411][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-12 16:04:47.412][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.413][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:04:47.414][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.415][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:47.416][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.417][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.417][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.418][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.419][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:04:47.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:47.421][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.422][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-12 16:04:47.423][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:47.424][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.425][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.426][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:47.426][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-12 16:04:47.426][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-12 16:04:47.426][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-12 16:04:47.426][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-12 16:04:47.427][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:47.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.429][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:47.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.432][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.432][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.433][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:47.434][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:47.435][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.436][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.437][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-12 16:04:47.439][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.439][self$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[2024-10-12 16:04:47.440][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.441][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:47.442][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.443][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.444][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.445][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.446][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-12 16:04:47.447][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:47.447][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.448][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-12 16:04:47.449][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:47.450][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.451][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.452][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.453][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:47.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.455][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:47.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.458][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.459][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.460][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:47.461][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:47.461][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.462][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.463][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-12 16:04:47.465][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.466][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-12 16:04:47.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.468][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:47.468][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.469][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.470][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.471][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.472][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-12 16:04:47.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:47.478][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.479][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-12 16:04:47.480][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:47.481][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.482][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.482][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.483][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-12 16:04:47.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.485][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.486][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:47.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.488][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.489][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.490][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:47.491][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:47.492][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.493][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.494][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:47.495][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.512][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[2024-10-12 16:04:47.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.565][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-12 16:04:47.566][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-12 16:04:47.567][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-12 16:04:47.569][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-12 16:04:47.570][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-12 16:04:47.571][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-12 16:04:47.573][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-12 16:04:47.574][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-12 16:04:47.575][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:04:47.576][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-12 16:04:47.578][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-12 16:04:47.579][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-12 16:04:47.580][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-12 16:04:47.581][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-12 16:04:47.583][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-12 16:04:47.584][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-12 16:04:47.585][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-12 16:04:47.586][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-12 16:04:47.588][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-12 16:04:47.589][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-12 16:04:47.590][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-12 16:04:47.591][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-12 16:04:47.593][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-12 16:04:47.594][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-12 16:04:47.595][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-12 16:04:47.596][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-12 16:04:47.598][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-12 16:04:47.599][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-12 16:04:47.600][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-12 16:04:47.601][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-12 16:04:47.603][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-12 16:04:47.604][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-12 16:04:47.605][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-12 16:04:47.607][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-12 16:04:47.608][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-12 16:04:47.609][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-12 16:04:47.610][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-12 16:04:47.611][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-12 16:04:47.613][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-12 16:04:47.614][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-12 16:04:47.615][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-12 16:04:47.617][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-12 16:04:47.618][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-12 16:04:47.619][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-12 16:04:47.620][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-12 16:04:47.622][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-12 16:04:47.623][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-12 16:04:47.624][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-12 16:04:47.625][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-12 16:04:47.627][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-12 16:04:47.628][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-12 16:04:47.629][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-12 16:04:47.630][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-12 16:04:47.632][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-12 16:04:47.633][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-12 16:04:47.634][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-12 16:04:47.635][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-12 16:04:47.637][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-12 16:04:47.638][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-12 16:04:47.643][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-12 16:04:47.645][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-12 16:04:47.646][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-12 16:04:47.647][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-12 16:04:47.648][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-12 16:04:47.650][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-12 16:04:47.651][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-12 16:04:47.652][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-12 16:04:47.653][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-12 16:04:47.655][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-12 16:04:47.656][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-12 16:04:47.657][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-12 16:04:47.658][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-12 16:04:47.660][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-12 16:04:47.661][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-12 16:04:47.662][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-12 16:04:47.664][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-12 16:04:47.665][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-12 16:04:47.666][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-12 16:04:47.667][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-12 16:04:47.669][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-12 16:04:47.670][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-12 16:04:47.671][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-12 16:04:47.672][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-12 16:04:47.674][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-12 16:04:47.675][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-12 16:04:47.676][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-12 16:04:47.677][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.678][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.769][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[2024-10-12 16:04:47.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-12 16:04:47.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-12 16:04:47.776][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-10-12 16:04:47.777][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:04:47.779][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.780][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-10-12 16:04:47.781][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.782][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-12 16:04:47.783][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.784][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.784][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.785][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.786][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-10-12 16:04:47.787][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-12 16:04:47.788][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.789][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-10-12 16:04:47.790][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-12 16:04:47.791][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-10-12 16:04:47.791][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:04:47.791][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:04:47.791][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-10-12 16:04:47.792][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-12 16:04:47.793][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-12 16:04:47.793][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-12 16:04:47.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.796][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-12 16:04:47.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-12 16:04:47.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-12 16:04:47.799][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-12 16:04:47.799][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-10-12 16:04:47.800][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-12 16:04:47.801][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-12 16:04:47.802][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-12 16:04:47.803][self$setPropertyValue]
biodb.DEBUG[2024-10-12 16:04:47.808][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-12 16:04:47.811][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:04:47.812][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-10-12 16:04:47.813][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-10-12 16:04:47.814][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-10-12 16:04:47.815][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:04:47.816][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-12 16:04:47.817][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-10-12 16:04:47.818][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-12 16:04:47.819][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-10-12 16:04:47.820][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-10-12 16:04:47.821][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-12 16:04:47.822][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-12 16:04:47.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-12 16:04:47.823][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-12 16:04:47.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-12 16:04:47.825][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-12 16:04:47.826][FUN] Functions in observer 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 1 | WARN 0 | SKIP 0 | PASS 84 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.8.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package ‘biodbExpasy’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** 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 (biodbExpasy)