Back to Long Tests report for BioC 3.20

This page was generated on 2024-06-08 23:55 -0400 (Sat, 08 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4672
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4407
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4434
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 7/32HostnameOS / ArchCHECK
biodbExpasy 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-08 09:55 -0400 (Sat, 08 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino4Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.4 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on merida1

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: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-06-08 16:01:14 -0400 (Sat, 08 Jun 2024)
EndedAt: 2024-06-08 16:06:23 -0400 (Sat, 08 Jun 2024)
EllapsedTime: 308.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-06-08 16:02:02.761][biodb::testContext]
biodb.INFO [2024-06-08 16:02:02.766][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:02:02.767][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-08 16:02:02.769][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:02:02.770][biodb::testContext]
biodb.INFO [2024-06-08 16:02:02.778][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-08 16:02:02.781][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:02:02.789][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:02:02.791][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:02:02.793][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:02:02.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.798][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:02:02.841][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:02:02.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.846][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:02:02.848][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:02:02.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.853][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:02:02.854][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:02:02.855][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:02:02.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.860][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:02:02.862][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:02:02.863][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:02:02.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.868][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:02:02.869][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:02:02.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.874][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:02:02.875][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:02:02.877][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:02:02.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.881][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:02:02.883][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:02:02.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.887][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:02:02.888][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:02:02.890][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:02:02.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.894][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:02:02.896][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:02:02.897][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:02:02.898][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:02:02.899][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:02:02.901][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:02:02.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.905][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:02:02.907][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:02:02.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.911][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:02:02.913][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:02:02.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.917][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:02:02.918][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:02:02.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.923][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:02:02.924][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:02:02.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.929][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:02:02.930][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:02:02.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.935][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:02:02.936][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:02:02.947][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:02:02.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.952][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:02:02.953][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:02:02.955][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:02:02.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:02.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:02.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:02.962][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:02:03.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.030][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:02:03.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:02:03.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.036][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.037][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.038][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.039][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:02:03.041][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:02:03.042][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.043][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:02:03.044][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:02:03.046][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.047][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.048][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:02:03.048][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:02:03.048][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:02:03.048][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:02:03.048][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:02:03.049][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:02:03.051][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.053][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:02:03.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.056][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.058][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:02:03.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:02:03.061][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.062][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.064][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:02:03.066][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.067][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:02:03.069][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.070][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:02:03.071][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.074][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.075][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.076][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:02:03.077][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:02:03.079][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.080][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:02:03.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:02:03.082][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.083][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.085][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:02:03.085][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:02:03.085][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:02:03.085][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:02:03.085][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:02:03.091][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:02:03.093][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.094][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.095][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:02:03.096][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.097][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.098][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.100][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.101][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:02:03.102][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:02:03.103][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.104][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.106][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:02:03.108][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.109][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:02:03.110][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.112][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:02:03.113][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.114][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.115][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.116][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.118][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:02:03.119][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:02:03.120][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.121][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:02:03.123][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:02:03.124][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.125][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.126][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.127][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:02:03.129][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.131][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:02:03.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.134][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.136][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.137][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:02:03.138][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:02:03.139][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.140][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.142][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:02:03.144][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.145][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:02:03.147][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.148][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:02:03.149][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.150][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.151][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.153][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.154][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:02:03.155][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:02:03.156][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.158][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:02:03.159][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:02:03.160][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.161][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.162][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.164][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:02:03.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.167][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:02:03.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.170][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.171][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.172][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.173][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:02:03.174][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:02:03.176][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.177][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.181][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:02:03.182][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.245][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.DEBUG[2024-06-08 16:02:03.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.280][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:02:03.285][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:02:03.287][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:02:03.289][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:02:03.290][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:02:03.292][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:02:03.294][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:02:03.296][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:02:03.297][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:02:03.299][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:02:03.301][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:02:03.302][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:02:03.304][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:02:03.306][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:02:03.308][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:02:03.309][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:02:03.311][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:02:03.313][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:02:03.315][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:02:03.316][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:02:03.318][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:02:03.320][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:02:03.322][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:02:03.329][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:02:03.331][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:02:03.332][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:02:03.334][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:02:03.336][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:02:03.338][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:02:03.339][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:02:03.341][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:02:03.343][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:02:03.345][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:02:03.346][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:02:03.348][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:02:03.350][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:02:03.351][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:02:03.353][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:02:03.355][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:02:03.357][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:02:03.358][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:02:03.360][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:02:03.362][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:02:03.364][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:02:03.366][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:02:03.367][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:02:03.369][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:02:03.371][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:02:03.372][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:02:03.374][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:02:03.376][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:02:03.378][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:02:03.379][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:02:03.381][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:02:03.383][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:02:03.385][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:02:03.386][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:02:03.388][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:02:03.390][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:02:03.391][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:02:03.393][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:02:03.395][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:02:03.396][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:02:03.398][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:02:03.400][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:02:03.402][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:02:03.403][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:02:03.405][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:02:03.407][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:02:03.408][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:02:03.410][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:02:03.412][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:02:03.413][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:02:03.415][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:02:03.417][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:02:03.418][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:02:03.420][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:02:03.422][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:02:03.424][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:02:03.425][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:02:03.427][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:02:03.429][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:02:03.430][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:02:03.438][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:02:03.440][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-08 16:02:03.444][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:02:03.445][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.447][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.500][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[2024-06-08 16:02:03.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.508][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[2024-06-08 16:02:03.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:02:03.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:03.592][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-08 16:02:03.606][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:02:03.609][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.610][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-08 16:02:03.611][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.613][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:02:03.614][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.615][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.616][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.617][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.619][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-08 16:02:03.620][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:02:03.621][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.622][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-08 16:02:03.624][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:02:03.625][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-08 16:02:03.625][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:02:03.625][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:02:03.625][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:02:03.626][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:02:03.628][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:02:03.629][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:02:03.630][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.631][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.632][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:02:03.634][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:02:03.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:02:03.636][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:02:03.637][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-08 16:02:03.638][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:02:03.639][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:02:03.641][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:02:03.642][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:02:03.650][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:02:03.673][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:02:03.674][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-08 16:02:03.679][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:02:03.683][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-08 16:02:03.688][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:02:03.689][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:02:03.691][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-08 16:02:03.702][biodb::testThat]
biodb.INFO [2024-06-08 16:02:03.703][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-08 16:02:03.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:02:03.706][biodb::testThat]
biodb.TRACE[2024-06-08 16:02:03.710][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-08 16:02:03.712][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:02:03.716][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-08 16:02:03.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:02:03.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:03.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:03.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:03.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:03.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:03.747][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.TRACE[2024-06-08 16:02:03.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:03.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:03.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.809][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:03.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:03.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.830][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.835][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:03.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:03.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.840][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:02:03.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.845][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.850][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.855][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.860][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:02:03.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:03.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:03.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:03.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:03.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:03.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:03.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:03.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:03.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:03.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:03.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:03.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.960][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:03.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:03.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.965][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:03.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:03.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:03.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:03.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.975][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:03.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:03.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:03.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:03.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:03.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:03.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:02:04.039][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-08 16:02:04.042][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:02:04.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:02:04.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.046][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:02:04.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:02:04.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.051][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:02:04.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:02:04.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.057][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:02:04.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:02:04.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.143][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.153][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.182][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.183][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.185][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.217][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.221][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.223][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.225][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.241][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.246][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.251][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.256][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.257][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.261][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.276][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.282][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.287][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.292][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.293][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.297][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.313][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.314][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.317][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.323][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.325][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.327][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.334][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.335][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.338][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.344][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.346][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.348][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.372][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-08 16:02:04.426][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:02:04.428][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-08 16:02:04.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:02:04.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:04.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:04.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:04.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:04.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:04.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:02:04.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.450][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.462][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:02:04.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:02:04.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.467][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.473][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.483][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:02:04.520][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-08 16:02:04.550][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:02:04.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:02:04.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:02:04.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:02:04.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.561][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:02:04.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:02:04.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.566][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:02:04.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:02:04.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.582][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.630][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.635][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.640][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:02:04.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.684][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.685][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.687][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.720][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.722][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.724][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.741][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.746][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.752][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.757][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.758][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.761][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.762][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.778][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:02:04.779][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:02:04.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.782][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.789][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.791][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:02:04.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.794][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:02:04.801][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:02:04.803][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:02:04.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:02:04.805][ef$get] fields variable is a list.
biodb.INFO [2024-06-08 16:02:04.821][biodb::testThat]
biodb.INFO [2024-06-08 16:02:04.822][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-08 16:02:04.824][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:02:04.825][biodb::testThat]
biodb.DEBUG[2024-06-08 16:02:04.828][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-08 16:02:04.836][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-08 16:02:04.842][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-08 16:02:04.845][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-08 16:02:04.847][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-08 16:02:04.849][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-08 16:02:04.850][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-08 16:02:04.852][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-08 16:02:04.854][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-08 16:02:04.855][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-08 16:02:04.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:02:04.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:02:04.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:02:04.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:02:04.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:02:04.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:02:04.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:02:04.875][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-08 16:02:04.904][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-08 16:02:04.906][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-08 16:02:04.907][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-08 16:02:40.337][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-08 16:03:12.282][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-08 16:03:12.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-08 16:03:12.305][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-08 16:03:12.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:03:12.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:12.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:12.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:12.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:12.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:12.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:12.349][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-08 16:03:12.371][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-08 16:03:12.372][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-08 16:03:12.403][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-08 16:03:39.391][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-08 16:04:01.081][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-08 16:04:01.084][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-08 16:04:01.088][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-08 16:04:01.092][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-06-08 16:04:01.094][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-08 16:04:01.096][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-08 16:04:01.097][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-08 16:04:01.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:04:01.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:04:01.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:04:01.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:04:01.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:04:01.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:04:01.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:04:01.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.120][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:04:01.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:04:01.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.131][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:04:01.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:04:01.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.156][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.161][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.166][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.177][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:01.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:04:01.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:04:01.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:04:01.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:04:01.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:04:01.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:04:01.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:04:01.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.225][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:04:01.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:04:01.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.235][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:04:01.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:04:01.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.240][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.245][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.255][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:01.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:01.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:01.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:01.306][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-08 16:04:01.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:04:01.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:04:01.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:04:01.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:04:01.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:04:01.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:04:01.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:04:01.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:04:01.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:04:01.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:04:01.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:04:01.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:04:01.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:04:01.351][biodb::testThat]
biodb.INFO [2024-06-08 16:04:01.352][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-08 16:04:01.353][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:01.355][biodb::testThat]
biodb.TRACE[2024-06-08 16:04:01.358][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.360][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.362][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:01.364][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-08 16:04:01.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:01.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:01.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:01.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:01.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:01.422][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-08 16:04:01.425][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-08 16:04:01.429][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-08 16:04:01.430][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-08 16:04:01.432][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-08 16:04:24.445][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-08 16:04:39.835][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-08 16:04:39.837][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-08 16:04:39.842][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-08 16:04:39.850][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-08 16:04:39.870][biodb::testThat]
biodb.INFO [2024-06-08 16:04:39.872][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-08 16:04:39.873][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:39.874][biodb::testThat]
biodb.TRACE[2024-06-08 16:04:39.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:39.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:39.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:39.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:39.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:39.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:39.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:39.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:39.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:39.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:39.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:39.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:39.964][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-08 16:04:39.968][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-08 16:04:39.989][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-08 16:04:39.991][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-08 16:04:39.992][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-08 16:04:40.014][biodb::testThat]
biodb.INFO [2024-06-08 16:04:40.015][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-08 16:04:40.016][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:40.017][biodb::testThat]
biodb.TRACE[2024-06-08 16:04:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:04:40.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:04:40.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:40.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:40.035][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:04:40.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:04:40.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:40.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:40.040][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:04:40.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:04:40.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:40.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:40.045][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:04:40.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:04:40.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:40.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:40.099][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:04:40.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:04:40.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:40.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:40.104][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:04:40.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:04:40.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:40.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:40.110][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:04:40.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:04:40.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:40.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:40.115][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:04:40.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:04:40.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:40.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:04:40.154][biodb::testThat]
biodb.INFO [2024-06-08 16:04:40.155][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-08 16:04:40.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:40.158][biodb::testThat]
biodb.INFO [2024-06-08 16:04:40.170][biodb::testThat]
biodb.INFO [2024-06-08 16:04:40.171][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-08 16:04:40.173][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:40.174][biodb::testThat]
biodb.INFO [2024-06-08 16:04:40.184][biodb::testThat]
biodb.INFO [2024-06-08 16:04:40.186][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-08 16:04:40.187][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:40.188][biodb::testThat]
biodb.DEBUG[2024-06-08 16:04:40.207][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[2024-06-08 16:05:02.920][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 [2024-06-08 16:05:17.644][biodb::testThat]
biodb.INFO [2024-06-08 16:05:17.646][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-08 16:05:17.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:05:17.648][biodb::testThat]
biodb.DEBUG[2024-06-08 16:05:49.516][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-08 16:06:21.748][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:21.750][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:21.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:21.752][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:06:21.754][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:06:21.755][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:06:21.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:06:21.758][ef$get] fields variable is a list.
biodb.INFO [2024-06-08 16:06:21.759][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:06:21.760][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-08 16:06:21.762][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-08 16:06:21.763][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:06:21.764][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:21.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:21.767][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:21.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:21.769][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-08 16:06:21.783][biodb::testContext]
biodb.INFO [2024-06-08 16:06:21.785][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:06:21.786][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-08 16:06:21.787][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:06:21.789][biodb::testContext]
biodb.INFO [2024-06-08 16:06:21.791][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-08 16:06:21.793][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:06:21.798][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:21.799][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:06:21.801][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:06:21.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.806][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:06:21.807][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:06:21.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.812][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:06:21.813][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:06:21.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.818][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:06:21.820][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:06:21.821][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:06:21.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.826][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:06:21.827][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:06:21.829][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:06:21.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.833][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:06:21.835][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:06:21.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.839][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:06:21.840][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:06:21.842][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:06:21.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.846][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:06:21.848][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:06:21.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.852][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:06:21.853][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:06:21.855][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:06:21.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.859][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:06:21.861][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:06:21.862][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:06:21.863][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:06:21.864][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:06:21.866][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:06:21.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.870][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:06:21.872][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:06:21.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.876][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:06:21.877][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:06:21.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.882][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:06:21.883][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:06:21.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.893][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:06:21.895][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:06:21.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.922][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:06:21.923][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:06:21.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.928][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:06:21.929][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:06:21.940][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:06:21.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.945][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:06:21.947][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:06:21.948][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:06:21.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:21.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:21.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:21.953][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:06:21.955][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:21.956][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:06:21.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:21.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:21.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:21.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:21.963][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:21.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:21.965][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:06:21.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:21.968][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:21.970][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:06:21.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:21.972][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:21.973][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:21.975][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:06:21.975][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:06:21.975][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:06:21.975][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:06:21.975][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:06:21.977][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:21.979][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:21.980][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:21.981][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:21.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:21.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:21.985][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:21.990][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:21.992][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:21.993][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:21.994][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:21.995][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:21.997][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:06:22.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.009][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:06:22.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.020][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:22.021][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.023][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.024][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.028][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.029][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:06:22.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:22.032][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.033][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:06:22.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:22.036][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.037][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.038][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:06:22.038][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:06:22.038][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:06:22.038][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:06:22.038][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:06:22.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:22.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:22.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:22.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:22.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:22.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:22.047][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.048][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:22.051][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:22.052][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.053][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.055][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:06:22.057][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.058][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:06:22.060][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.061][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:22.062][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.064][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.065][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.066][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.067][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:06:22.069][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:22.070][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.072][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:06:22.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:22.074][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.077][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:22.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:22.081][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:22.082][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:22.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:22.084][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:22.086][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.092][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:22.094][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:22.096][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.097][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.099][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:06:22.101][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.102][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:06:22.104][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.105][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:22.106][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.108][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.109][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.110][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.112][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:06:22.113][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:22.114][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.115][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:06:22.117][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:22.118][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.119][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.120][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.122][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:06:22.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:22.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:22.125][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:22.126][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:22.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:22.129][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.130][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.131][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:22.132][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:22.133][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.135][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.136][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:22.137][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.241][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:06:22.243][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:06:22.244][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:06:22.246][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:06:22.248][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:06:22.249][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:06:22.251][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:06:22.253][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:06:22.254][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:06:22.256][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:06:22.258][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:06:22.259][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:06:22.261][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:06:22.263][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:06:22.264][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:06:22.266][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:06:22.268][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:06:22.270][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:06:22.271][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:06:22.273][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:06:22.275][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:06:22.276][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:06:22.278][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:06:22.280][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:06:22.282][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:06:22.283][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:06:22.285][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:06:22.287][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:06:22.289][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:06:22.291][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:06:22.293][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:06:22.294][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:06:22.296][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:06:22.298][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:06:22.300][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:06:22.302][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:06:22.303][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:06:22.305][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:06:22.307][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:06:22.309][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:06:22.311][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:06:22.313][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:06:22.315][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:06:22.317][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:06:22.319][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:06:22.321][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:06:22.322][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:06:22.324][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:06:22.326][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:06:22.328][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:06:22.330][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:06:22.331][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:06:22.333][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:06:22.335][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:06:22.337][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:06:22.338][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:06:22.340][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:06:22.342][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:06:22.344][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:06:22.346][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:06:22.347][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:06:22.349][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:06:22.351][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:06:22.353][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:06:22.355][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:06:22.357][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:06:22.358][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:06:22.360][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:06:22.362][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:06:22.368][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:06:22.370][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:06:22.372][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:06:22.374][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:06:22.376][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:06:22.378][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:06:22.380][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:06:22.381][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:06:22.383][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:06:22.385][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:06:22.387][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:06:22.389][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:06:22.390][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:06:22.392][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:06:22.400][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:06:22.402][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-08 16:06:22.403][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:06:22.405][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.407][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:06:22.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:06:22.549][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-08 16:06:22.551][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:06:22.554][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.555][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-08 16:06:22.557][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.558][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:06:22.559][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.560][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.562][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.563][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.565][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-08 16:06:22.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:06:22.592][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.593][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-08 16:06:22.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:06:22.596][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-08 16:06:22.596][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:06:22.596][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:06:22.596][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:06:22.597][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:06:22.599][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:06:22.600][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:06:22.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:22.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:22.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:06:22.605][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:06:22.606][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:06:22.607][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:06:22.608][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-08 16:06:22.610][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:06:22.611][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:06:22.612][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:06:22.613][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:06:22.615][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:06:22.619][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:06:22.620][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-08 16:06:22.622][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:06:22.623][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-08 16:06:22.625][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:06:22.626][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:06:22.627][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-08 16:06:22.629][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:06:22.630][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-08 16:06:22.632][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-08 16:06:22.633][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:06:22.634][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:06:22.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:06:22.636][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:06:22.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:06:22.638][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:06:22.639][FUN] Functions in observer 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 85 ]

══ 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 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* 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 ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 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 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-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)