Back to Long Tests report for BioC 3.20

This page was generated on 2025-01-18 23:55 -0500 (Sat, 18 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4489
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
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 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-01-18 09:55 -0500 (Sat, 18 Jan 2025)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_20
git_last_commit: 4403c2f
git_last_commit_date: 2024-10-29 11:09:35 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on nebbiolo2

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: 1.10.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
StartedAt: 2025-01-18 16:01:50 -0500 (Sat, 18 Jan 2025)
EndedAt: 2025-01-18 16:02:34 -0500 (Sat, 18 Jan 2025)
EllapsedTime: 44.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2025-01-18 16:02:25.899][biodb::testContext]
biodb.INFO [2025-01-18 16:02:25.901][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-18 16:02:25.902][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-18 16:02:25.903][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-18 16:02:25.904][biodb::testContext]
biodb.INFO [2025-01-18 16:02:25.910][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-18 16:02:25.912][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-18 16:02:25.919][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:02:25.921][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-18 16:02:25.922][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-18 16:02:25.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.925][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-18 16:02:25.945][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-18 16:02:25.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.949][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-18 16:02:25.950][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-18 16:02:25.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.953][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-18 16:02:25.954][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-18 16:02:25.955][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-18 16:02:25.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.958][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[2025-01-18 16:02:25.959][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-18 16:02:25.960][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-18 16:02:25.961][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-18 16:02:25.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.965][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-18 16:02:25.966][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-18 16:02:25.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.970][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-18 16:02:25.971][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-18 16:02:25.972][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-18 16:02:25.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.975][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-18 16:02:25.976][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-18 16:02:25.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.980][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-18 16:02:25.981][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-18 16:02:25.982][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-18 16:02:25.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.986][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-18 16:02:25.987][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-18 16:02:25.988][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-18 16:02:25.989][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-18 16:02:25.990][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-18 16:02:25.991][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-18 16:02:25.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.995][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-18 16:02:25.996][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-18 16:02:25.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:25.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:25.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:25.999][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-18 16:02:26.001][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-18 16:02:26.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.004][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-18 16:02:26.005][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-18 16:02:26.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.009][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-18 16:02:26.010][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-18 16:02:26.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.014][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-18 16:02:26.015][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-18 16:02:26.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.018][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-18 16:02:26.020][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-18 16:02:26.024][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-18 16:02:26.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.027][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-18 16:02:26.028][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-18 16:02:26.030][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-18 16:02:26.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.036][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-18 16:02:26.072][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.095][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-18 16:02:26.096][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.097][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:26.098][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.099][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.099][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.100][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.101][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-18 16:02:26.102][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:26.103][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.104][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-18 16:02:26.105][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:26.106][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.106][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.107][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:02:26.107][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-18 16:02:26.107][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-18 16:02:26.107][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-18 16:02:26.107][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-18 16:02:26.108][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:02:26.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:26.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.113][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.114][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:26.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:26.117][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.117][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.118][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-18 16:02:26.120][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.121][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-18 16:02:26.122][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.123][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:26.124][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.124][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.125][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.126][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.127][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-18 16:02:26.128][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:26.129][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.130][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-18 16:02:26.131][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:26.131][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.132][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.133][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:02:26.133][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-18 16:02:26.133][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-18 16:02:26.133][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-18 16:02:26.133][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-18 16:02:26.134][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:02:26.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.136][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.137][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:26.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.140][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.141][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:26.141][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:26.142][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.143][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.144][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-18 16:02:26.146][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.147][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-18 16:02:26.147][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.148][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:26.149][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.150][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.151][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.152][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.153][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-18 16:02:26.154][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:26.154][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.155][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-18 16:02:26.156][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:26.157][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.158][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.159][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.160][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:02:26.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.162][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:26.163][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.165][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.165][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.166][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:26.167][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:26.168][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.169][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.170][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-18 16:02:26.171][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.172][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-18 16:02:26.173][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.174][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:26.175][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.176][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.176][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.177][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.178][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-18 16:02:26.179][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:26.180][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.181][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-18 16:02:26.182][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:26.183][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.183][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.184][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.185][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:02:26.186][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.187][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.188][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:26.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.190][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.191][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:26.193][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:26.193][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.194][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.198][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:02:26.198][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.207][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[2025-01-18 16:02:26.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.211][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[2025-01-18 16:02:26.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.223][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[2025-01-18 16:02:26.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.234][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[2025-01-18 16:02:26.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.266][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-18 16:02:26.270][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-18 16:02:26.272][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-18 16:02:26.273][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-18 16:02:26.274][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-18 16:02:26.275][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-18 16:02:26.276][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-18 16:02:26.278][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-18 16:02:26.279][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-18 16:02:26.280][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-18 16:02:26.281][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-18 16:02:26.283][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-18 16:02:26.284][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-18 16:02:26.285][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-18 16:02:26.286][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-18 16:02:26.288][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-18 16:02:26.289][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-18 16:02:26.290][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-18 16:02:26.291][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-18 16:02:26.293][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-18 16:02:26.294][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-18 16:02:26.295][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-18 16:02:26.296][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-18 16:02:26.306][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-18 16:02:26.307][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-18 16:02:26.309][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-18 16:02:26.310][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-18 16:02:26.311][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-18 16:02:26.313][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-18 16:02:26.314][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-18 16:02:26.316][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-18 16:02:26.317][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-18 16:02:26.318][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-18 16:02:26.320][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-18 16:02:26.321][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-18 16:02:26.323][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-18 16:02:26.342][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-18 16:02:26.344][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-18 16:02:26.345][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-18 16:02:26.347][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-18 16:02:26.348][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-18 16:02:26.349][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-18 16:02:26.351][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-18 16:02:26.352][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-18 16:02:26.353][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-18 16:02:26.355][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-18 16:02:26.356][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-18 16:02:26.358][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-18 16:02:26.359][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-18 16:02:26.361][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-18 16:02:26.362][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-18 16:02:26.363][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-18 16:02:26.365][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-18 16:02:26.366][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-18 16:02:26.368][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-18 16:02:26.369][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-18 16:02:26.370][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-18 16:02:26.372][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-18 16:02:26.374][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-18 16:02:26.375][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-18 16:02:26.376][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-18 16:02:26.378][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-18 16:02:26.379][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-18 16:02:26.380][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-18 16:02:26.382][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-18 16:02:26.383][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-18 16:02:26.385][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-18 16:02:26.386][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-18 16:02:26.387][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-18 16:02:26.389][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-18 16:02:26.390][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-18 16:02:26.391][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-18 16:02:26.393][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-18 16:02:26.394][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-18 16:02:26.395][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-18 16:02:26.397][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-18 16:02:26.398][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-18 16:02:26.399][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-18 16:02:26.401][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-18 16:02:26.402][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-18 16:02:26.404][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-18 16:02:26.405][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-18 16:02:26.406][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-18 16:02:26.412][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-18 16:02:26.414][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-18 16:02:26.417][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:02:26.418][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.420][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.508][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[2025-01-18 16:02:26.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:26.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:26.528][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-01-18 16:02:26.537][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-01-18 16:02:26.539][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.540][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-01-18 16:02:26.541][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.542][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:26.543][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.544][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.545][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.546][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.547][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-01-18 16:02:26.548][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:26.549][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.550][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-01-18 16:02:26.550][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:26.551][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-01-18 16:02:26.551][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-01-18 16:02:26.551][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-01-18 16:02:26.551][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-01-18 16:02:26.552][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:26.553][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:02:26.554][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-18 16:02:26.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.557][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:26.558][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:26.559][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:26.560][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:26.561][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-01-18 16:02:26.562][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:26.562][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:26.563][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:26.564][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:26.570][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-18 16:02:26.595][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-01-18 16:02:26.596][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-01-18 16:02:26.600][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-01-18 16:02:26.603][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-01-18 16:02:26.607][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-18 16:02:26.608][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-18 16:02:26.609][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-01-18 16:02:26.617][biodb::testThat]
biodb.INFO [2025-01-18 16:02:26.617][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-18 16:02:26.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:26.619][biodb::testThat]
biodb.TRACE[2025-01-18 16:02:26.622][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2025-01-18 16:02:26.624][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-01-18 16:02:26.627][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-01-18 16:02:26.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-18 16:02:26.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:26.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:26.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:26.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:26.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:26.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-18 16:02:26.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.686][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:26.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:26.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.701][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.708][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-18 16:02:26.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.712][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.715][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.719][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.722][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-18 16:02:26.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.741][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.745][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.789][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.799][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:02:26.832][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2025-01-18 16:02:26.834][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:02:26.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:02:26.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.837][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:02:26.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:02:26.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-18 16:02:26.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-18 16:02:26.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.844][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-18 16:02:26.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-18 16:02:26.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.875][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.904][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.908][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.911][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:26.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.931][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.931][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.933][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:26.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:26.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.944][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.954][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.955][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.957][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:26.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:26.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.967][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.971][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.974][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.978][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.979][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.981][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.981][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:26.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.991][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:26.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:26.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.995][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:26.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:26.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:26.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:26.998][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:26.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.002][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.003][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.004][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.005][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.037][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.040][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.044][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.045][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.046][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.050][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-18 16:02:27.051][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:27.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.053][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.056][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:27.057][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:27.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.059][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.074][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2025-01-18 16:02:27.105][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-01-18 16:02:27.106][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-01-18 16:02:27.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-18 16:02:27.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:27.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:27.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:27.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:27.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:27.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-18 16:02:27.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.120][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.124][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:27.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:27.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.128][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-18 16:02:27.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:27.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.131][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.135][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.142][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:02:27.166][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2025-01-18 16:02:27.184][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:02:27.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:02:27.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:02:27.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:02:27.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-18 16:02:27.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-18 16:02:27.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.195][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-18 16:02:27.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-18 16:02:27.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.205][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.238][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.241][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.245][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:27.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.273][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.274][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.276][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:27.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:27.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.290][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:27.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:27.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:27.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:27.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.297][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:27.298][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:27.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.299][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:27.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:27.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.310][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.313][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.317][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.320][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.321][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.323][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.324][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.333][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:27.334][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:27.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.336][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.340][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.341][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:27.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.342][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:27.346][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:27.347][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:27.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:27.348][ef$get] fields variable is a list.
biodb.INFO [2025-01-18 16:02:27.354][biodb::testThat]
biodb.INFO [2025-01-18 16:02:27.355][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-18 16:02:27.356][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:27.357][biodb::testThat]
biodb.DEBUG[2025-01-18 16:02:27.359][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2025-01-18 16:02:27.365][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2025-01-18 16:02:27.369][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.TRACE[2025-01-18 16:02:27.370][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2025-01-18 16:02:27.372][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt".
biodb.DEBUG[2025-01-18 16:02:27.373][conn$getEntryContent] 1 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2025-01-18 16:02:27.374][conn$getEntryContent] 1 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2025-01-18 16:02:27.375][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-18 16:02:27.375][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-18 16:02:27.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-18 16:02:27.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:27.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:27.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:27.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:27.386][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:27.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:27.388][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2025-01-18 16:02:27.411][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-18 16:02:27.412][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-18 16:02:27.413][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2025-01-18 16:02:28.184][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2025-01-18 16:02:28.813][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-18 16:02:28.817][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2025-01-18 16:02:28.849][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2025-01-18 16:02:28.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2025-01-18 16:02:28.857][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-18 16:02:28.859][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2025-01-18 16:02:28.861][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2025-01-18 16:02:28.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-18 16:02:28.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:28.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:28.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:28.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:28.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:28.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-18 16:02:28.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.884][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:28.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:28.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:28.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:28.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.893][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-18 16:02:28.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:28.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:28.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:28.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:28.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:28.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:28.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:28.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:28.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:28.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:28.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:28.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.916][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.920][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.927][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:02:28.953][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-18 16:02:28.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:28.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:28.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:28.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:28.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:28.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-18 16:02:28.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.967][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:28.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-18 16:02:28.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:28.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:28.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.974][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-18 16:02:28.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-18 16:02:28.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.978][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.981][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.989][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-18 16:02:28.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:28.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:28.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:29.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:29.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:29.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:29.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:29.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:29.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:29.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:29.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:29.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:29.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:29.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:29.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:02:29.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:02:29.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:02:29.024][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2025-01-18 16:02:29.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-18 16:02:29.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-18 16:02:29.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-18 16:02:29.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-18 16:02:29.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-18 16:02:29.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-18 16:02:29.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-18 16:02:29.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-18 16:02:29.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-18 16:02:29.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-18 16:02:29.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-18 16:02:29.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-18 16:02:29.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-18 16:02:29.057][biodb::testThat]
biodb.INFO [2025-01-18 16:02:29.057][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-18 16:02:29.058][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:29.059][biodb::testThat]
biodb.TRACE[2025-01-18 16:02:29.062][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:29.063][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:29.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.064][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:02:29.066][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2025-01-18 16:02:29.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:29.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:29.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:29.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:29.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:29.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:02:29.100][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2025-01-18 16:02:29.123][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-01-18 16:02:29.137][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-18 16:02:29.138][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-18 16:02:29.152][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2025-01-18 16:02:29.612][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2025-01-18 16:02:30.009][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-18 16:02:30.014][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2025-01-18 16:02:30.021][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2025-01-18 16:02:30.034][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2025-01-18 16:02:30.060][biodb::testThat]
biodb.INFO [2025-01-18 16:02:30.062][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-18 16:02:30.064][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:30.065][biodb::testThat]
biodb.TRACE[2025-01-18 16:02:30.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:30.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:30.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:30.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:30.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:30.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:02:30.128][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-01-18 16:02:30.131][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-18 16:02:30.145][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2025-01-18 16:02:30.146][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-18 16:02:30.147][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2025-01-18 16:02:30.168][biodb::testThat]
biodb.INFO [2025-01-18 16:02:30.169][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-18 16:02:30.170][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:30.170][biodb::testThat]
biodb.TRACE[2025-01-18 16:02:30.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:02:30.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:02:30.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:02:30.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:02:30.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.186][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-18 16:02:30.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-18 16:02:30.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.189][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-18 16:02:30.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-18 16:02:30.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.222][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:02:30.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:02:30.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.225][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:02:30.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:02:30.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.229][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-18 16:02:30.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-18 16:02:30.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:30.233][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-18 16:02:30.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-18 16:02:30.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:30.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-18 16:02:30.240][biodb::testThat]
biodb.INFO [2025-01-18 16:02:30.241][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-18 16:02:30.242][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:30.243][biodb::testThat]
biodb.INFO [2025-01-18 16:02:30.250][biodb::testThat]
biodb.INFO [2025-01-18 16:02:30.251][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-18 16:02:30.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:30.253][biodb::testThat]
biodb.INFO [2025-01-18 16:02:30.259][biodb::testThat]
biodb.INFO [2025-01-18 16:02:30.260][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-18 16:02:30.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:30.262][biodb::testThat]
biodb.DEBUG[2025-01-18 16:02:30.274][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[2025-01-18 16:02:30.657][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 [2025-01-18 16:02:31.127][biodb::testThat]
biodb.INFO [2025-01-18 16:02:31.131][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-18 16:02:31.133][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:02:31.135][biodb::testThat]
biodb.DEBUG[2025-01-18 16:02:31.519][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2025-01-18 16:02:32.306][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:32.309][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:32.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:32.313][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:02:32.315][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:02:32.316][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:02:32.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:02:32.320][ef$get] fields variable is a list.
biodb.INFO [2025-01-18 16:02:32.321][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-18 16:02:32.323][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-01-18 16:02:32.325][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-01-18 16:02:32.326][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-18 16:02:32.328][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.330][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.354][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-18 16:02:32.365][biodb::testContext]
biodb.INFO [2025-01-18 16:02:32.366][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-18 16:02:32.367][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-01-18 16:02:32.368][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-18 16:02:32.368][biodb::testContext]
biodb.INFO [2025-01-18 16:02:32.370][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-18 16:02:32.372][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-18 16:02:32.376][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:02:32.377][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-18 16:02:32.378][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-18 16:02:32.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.382][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-18 16:02:32.383][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-18 16:02:32.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.386][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-18 16:02:32.387][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-18 16:02:32.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.391][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-18 16:02:32.392][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-18 16:02:32.393][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-18 16:02:32.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.396][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-18 16:02:32.397][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-18 16:02:32.398][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-18 16:02:32.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.402][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-18 16:02:32.403][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-18 16:02:32.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.407][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-18 16:02:32.407][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-18 16:02:32.409][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-18 16:02:32.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.412][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-18 16:02:32.413][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-18 16:02:32.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.417][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-18 16:02:32.418][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-18 16:02:32.419][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-18 16:02:32.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.422][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-18 16:02:32.423][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-18 16:02:32.424][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-18 16:02:32.425][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-18 16:02:32.426][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-18 16:02:32.427][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-18 16:02:32.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.431][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-18 16:02:32.432][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-18 16:02:32.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.435][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-18 16:02:32.436][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-18 16:02:32.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.440][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-18 16:02:32.441][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-18 16:02:32.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.444][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-18 16:02:32.445][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-18 16:02:32.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.449][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-18 16:02:32.450][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-18 16:02:32.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.453][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-18 16:02:32.454][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-18 16:02:32.458][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-18 16:02:32.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.461][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-18 16:02:32.462][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-18 16:02:32.463][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-18 16:02:32.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.467][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-18 16:02:32.469][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.470][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-18 16:02:32.471][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.472][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:32.473][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.474][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.475][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.476][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.477][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-18 16:02:32.478][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:32.479][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.480][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-18 16:02:32.481][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:32.482][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.483][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.483][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:02:32.483][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-18 16:02:32.483][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-18 16:02:32.483][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-18 16:02:32.483][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-18 16:02:32.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:02:32.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.486][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.487][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:32.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.489][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.490][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.491][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:32.492][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:32.493][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.494][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.495][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-18 16:02:32.496][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.497][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-18 16:02:32.498][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:32.500][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.501][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.502][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.503][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.504][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-18 16:02:32.505][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:32.506][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.506][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-18 16:02:32.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:32.508][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.509][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.510][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:02:32.510][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-18 16:02:32.510][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-18 16:02:32.510][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-18 16:02:32.510][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-18 16:02:32.511][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:02:32.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.513][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:32.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.517][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.518][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:32.518][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:32.519][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.520][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.521][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-18 16:02:32.523][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.524][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-18 16:02:32.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:32.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.532][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.534][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-18 16:02:32.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:32.536][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.537][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-18 16:02:32.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:32.539][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.540][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.541][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.541][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:02:32.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:32.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.547][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.547][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.548][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:32.549][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:32.550][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.551][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.552][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-18 16:02:32.554][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.554][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-18 16:02:32.555][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.556][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:32.557][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.559][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.561][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-18 16:02:32.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:32.563][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.563][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-18 16:02:32.564][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:32.565][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.566][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.567][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.568][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:02:32.569][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.570][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.570][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:32.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.573][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.574][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.575][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:32.575][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:32.576][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.577][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.578][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:02:32.579][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.649][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-18 16:02:32.650][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-18 16:02:32.651][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-18 16:02:32.653][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-18 16:02:32.654][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-18 16:02:32.655][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-18 16:02:32.656][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-18 16:02:32.658][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-18 16:02:32.659][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-18 16:02:32.660][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-18 16:02:32.661][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-18 16:02:32.663][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-18 16:02:32.664][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-18 16:02:32.665][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-18 16:02:32.666][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-18 16:02:32.668][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-18 16:02:32.669][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-18 16:02:32.670][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-18 16:02:32.672][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-18 16:02:32.673][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-18 16:02:32.674][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-18 16:02:32.675][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-18 16:02:32.677][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-18 16:02:32.678][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-18 16:02:32.679][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-18 16:02:32.680][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-18 16:02:32.682][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-18 16:02:32.683][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-18 16:02:32.684][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-18 16:02:32.685][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-18 16:02:32.687][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-18 16:02:32.688][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-18 16:02:32.689][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-18 16:02:32.695][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-18 16:02:32.696][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-18 16:02:32.697][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-18 16:02:32.698][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-18 16:02:32.700][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-18 16:02:32.701][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-18 16:02:32.702][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-18 16:02:32.704][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-18 16:02:32.705][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-18 16:02:32.706][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-18 16:02:32.707][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-18 16:02:32.709][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-18 16:02:32.710][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-18 16:02:32.711][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-18 16:02:32.712][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-18 16:02:32.714][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-18 16:02:32.715][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-18 16:02:32.716][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-18 16:02:32.718][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-18 16:02:32.719][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-18 16:02:32.720][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-18 16:02:32.721][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-18 16:02:32.722][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-18 16:02:32.724][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-18 16:02:32.725][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-18 16:02:32.726][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-18 16:02:32.727][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-18 16:02:32.729][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-18 16:02:32.730][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-18 16:02:32.731][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-18 16:02:32.732][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-18 16:02:32.734][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-18 16:02:32.735][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-18 16:02:32.736][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-18 16:02:32.737][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-18 16:02:32.739][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-18 16:02:32.740][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-18 16:02:32.741][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-18 16:02:32.742][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-18 16:02:32.744][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-18 16:02:32.745][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-18 16:02:32.746][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-18 16:02:32.747][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-18 16:02:32.749][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-18 16:02:32.750][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-18 16:02:32.751][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-18 16:02:32.752][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-18 16:02:32.754][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-18 16:02:32.755][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-18 16:02:32.756][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-18 16:02:32.757][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-18 16:02:32.759][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-18 16:02:32.760][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:02:32.761][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.762][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:02:32.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:02:32.863][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-01-18 16:02:32.864][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-01-18 16:02:32.866][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.867][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-01-18 16:02:32.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.869][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:02:32.870][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.871][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.872][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.872][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.873][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-01-18 16:02:32.874][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:02:32.875][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.876][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-01-18 16:02:32.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:02:32.878][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-01-18 16:02:32.878][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-01-18 16:02:32.878][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-01-18 16:02:32.878][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-01-18 16:02:32.879][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-18 16:02:32.880][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:02:32.881][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-18 16:02:32.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:02:32.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:02:32.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:02:32.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:02:32.887][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-01-18 16:02:32.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:02:32.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:02:32.889][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-18 16:02:32.890][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:02:32.891][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-18 16:02:32.894][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-01-18 16:02:32.895][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-01-18 16:02:32.896][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-01-18 16:02:32.898][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-01-18 16:02:32.899][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-18 16:02:32.900][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-18 16:02:32.901][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-01-18 16:02:32.902][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-18 16:02:32.903][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-01-18 16:02:32.904][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-01-18 16:02:32.904][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-18 16:02:32.905][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:02:32.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:02:32.907][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:02:32.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:02:32.908][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:02:32.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.10.0’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 84 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-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
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)