Back to Long Tests report for BioC 3.18

This page was generated on 2024-03-02 23:55:02 -0500 (Sat, 02 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 7/30HostnameOS / ArchCHECK
biodbExpasy 1.6.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-03-02 09:55:02 -0500 (Sat, 02 Mar 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_18
git_last_commit: abe7f92
git_last_commit_date: 2023-10-24 11:40:32 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbExpasy on lconway


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: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.6.0.tar.gz
StartedAt: 2024-03-02 15:00:50 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 15:01:43 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 52.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-03-02 15:01:29.905][biodb::testContext]
biodb.INFO [2024-03-02 15:01:29.909][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 15:01:29.910][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-03-02 15:01:29.911][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 15:01:29.911][biodb::testContext]
biodb.INFO [2024-03-02 15:01:29.917][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-02 15:01:29.919][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 15:01:29.926][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:29.927][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 15:01:29.928][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 15:01:29.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.932][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 15:01:29.948][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 15:01:29.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.952][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 15:01:29.953][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 15:01:29.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.957][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 15:01:29.957][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 15:01:29.958][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 15:01:29.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.961][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.DEBUG[2024-03-02 15:01:29.962][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 15:01:29.963][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 15:01:29.964][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 15:01:29.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.967][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 15:01:29.968][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 15:01:29.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.971][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 15:01:29.972][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 15:01:29.973][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 15:01:29.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.977][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 15:01:29.978][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 15:01:29.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.981][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 15:01:29.982][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 15:01:29.983][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 15:01:29.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.986][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 15:01:29.987][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 15:01:29.988][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 15:01:29.989][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 15:01:29.990][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 15:01:29.991][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 15:01:29.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.994][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 15:01:29.995][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 15:01:29.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:29.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:29.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:29.999][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 15:01:30.000][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 15:01:30.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.003][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 15:01:30.004][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 15:01:30.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.007][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 15:01:30.008][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 15:01:30.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.012][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 15:01:30.013][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 15:01:30.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.016][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 15:01:30.017][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 15:01:30.043][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 15:01:30.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.046][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 15:01:30.047][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 15:01:30.048][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 15:01:30.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.055][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 15:01:30.086][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.105][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 15:01:30.106][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.107][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:30.108][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.109][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.110][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.110][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.111][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 15:01:30.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:30.113][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.114][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 15:01:30.114][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:30.115][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.116][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.117][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:30.117][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 15:01:30.117][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 15:01:30.117][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 15:01:30.117][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 15:01:30.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:30.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.119][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.120][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:30.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.122][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.123][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.124][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:30.125][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:30.125][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.126][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.127][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 15:01:30.129][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.130][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 15:01:30.130][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.131][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:30.132][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.133][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.134][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.134][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.135][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 15:01:30.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:30.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.138][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 15:01:30.138][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:30.139][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.140][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.141][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:30.141][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 15:01:30.141][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 15:01:30.141][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 15:01:30.141][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 15:01:30.142][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:30.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.144][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:30.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.146][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.147][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.148][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:30.149][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:30.149][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.150][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.151][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 15:01:30.153][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.153][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 15:01:30.154][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.155][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:30.156][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.157][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.157][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.158][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.159][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 15:01:30.160][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:30.161][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.161][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 15:01:30.162][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:30.163][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.164][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.165][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:30.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.168][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:30.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.171][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.172][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:30.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:30.173][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.174][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.175][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 15:01:30.176][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.177][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 15:01:30.178][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.179][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:30.180][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.180][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.181][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.182][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.183][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 15:01:30.184][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:30.185][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.185][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 15:01:30.186][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:30.187][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.188][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.189][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.190][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:30.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.192][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:30.193][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.194][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.195][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.196][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.196][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:30.197][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:30.198][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.199][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.202][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:30.203][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.215][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[2024-03-02 15:01:30.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.270][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 15:01:30.275][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 15:01:30.276][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 15:01:30.277][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 15:01:30.279][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 15:01:30.280][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 15:01:30.281][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 15:01:30.282][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 15:01:30.283][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 15:01:30.284][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 15:01:30.285][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 15:01:30.286][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 15:01:30.288][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 15:01:30.289][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 15:01:30.290][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 15:01:30.291][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 15:01:30.292][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 15:01:30.294][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 15:01:30.295][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 15:01:30.296][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 15:01:30.301][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 15:01:30.303][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 15:01:30.304][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 15:01:30.305][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 15:01:30.306][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 15:01:30.307][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 15:01:30.308][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 15:01:30.309][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 15:01:30.310][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 15:01:30.311][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 15:01:30.313][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 15:01:30.314][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 15:01:30.315][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 15:01:30.316][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 15:01:30.317][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 15:01:30.318][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 15:01:30.319][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 15:01:30.320][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 15:01:30.321][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 15:01:30.322][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 15:01:30.323][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 15:01:30.325][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 15:01:30.326][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 15:01:30.327][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 15:01:30.328][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 15:01:30.329][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 15:01:30.330][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 15:01:30.331][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 15:01:30.333][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 15:01:30.334][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 15:01:30.335][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 15:01:30.336][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 15:01:30.337][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 15:01:30.338][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 15:01:30.339][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 15:01:30.340][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 15:01:30.342][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 15:01:30.343][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 15:01:30.344][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 15:01:30.345][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 15:01:30.346][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 15:01:30.347][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 15:01:30.348][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 15:01:30.350][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 15:01:30.351][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 15:01:30.352][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 15:01:30.353][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 15:01:30.354][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 15:01:30.355][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 15:01:30.356][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 15:01:30.357][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 15:01:30.358][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 15:01:30.360][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 15:01:30.361][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 15:01:30.362][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 15:01:30.363][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 15:01:30.364][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 15:01:30.365][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 15:01:30.366][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 15:01:30.367][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 15:01:30.369][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 15:01:30.370][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 15:01:30.371][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 15:01:30.375][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 15:01:30.377][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-02 15:01:30.380][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:30.380][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.382][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.411][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[2024-03-02 15:01:30.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.416][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[2024-03-02 15:01:30.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.421][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[2024-03-02 15:01:30.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.466][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[2024-03-02 15:01:30.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:30.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:30.473][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-03-02 15:01:30.480][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-03-02 15:01:30.482][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.483][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-03-02 15:01:30.484][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.484][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:30.485][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.486][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.487][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.488][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-03-02 15:01:30.489][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:30.490][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.495][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-03-02 15:01:30.496][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:30.497][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-03-02 15:01:30.497][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-03-02 15:01:30.497][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-03-02 15:01:30.497][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-03-02 15:01:30.497][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:30.498][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:30.499][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 15:01:30.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.501][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:30.502][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:30.503][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:30.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:30.504][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-03-02 15:01:30.505][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:30.506][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:30.507][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:30.507][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:30.512][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 15:01:30.532][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-03-02 15:01:30.533][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-03-02 15:01:30.537][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-03-02 15:01:30.541][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-03-02 15:01:30.544][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 15:01:30.545][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 15:01:30.546][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-03-02 15:01:30.554][biodb::testThat]
biodb.INFO [2024-03-02 15:01:30.555][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-03-02 15:01:30.556][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:30.557][biodb::testThat]
biodb.TRACE[2024-03-02 15:01:30.560][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-03-02 15:01:30.561][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-03-02 15:01:30.564][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-03-02 15:01:30.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:30.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:30.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:30.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:30.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:30.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:30.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 15:01:30.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.619][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.632][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.639][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-03-02 15:01:30.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.642][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.645][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.648][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.652][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-03-02 15:01:30.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.718][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.721][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.727][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:30.750][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-03-02 15:01:30.752][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:30.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:30.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.755][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:30.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:30.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.758][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:30.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:30.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.762][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:30.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:30.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.792][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.821][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.825][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.828][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:30.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.848][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.849][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.850][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.872][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.873][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.874][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.890][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.894][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.897][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.900][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.901][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.902][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.903][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.913][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.917][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.920][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.924][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.924][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.926][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.927][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.938][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:30.939][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:30.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.940][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.945][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.946][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:30.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.947][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.952][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.953][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:30.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.954][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.959][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:30.960][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:30.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:30.961][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:30.975][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-03-02 15:01:31.002][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-03-02 15:01:31.003][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-03-02 15:01:31.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:31.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:31.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:31.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:31.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:31.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:31.013][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.TRACE[2024-03-02 15:01:31.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.018][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:31.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:31.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.025][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-03-02 15:01:31.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:31.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.029][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.032][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.039][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:31.084][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-03-02 15:01:31.100][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:31.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:31.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.104][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:31.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:31.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:31.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:31.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.110][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:31.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:31.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.122][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.150][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.153][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.157][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:31.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.184][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.185][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.186][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:31.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:31.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:31.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:31.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:31.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:31.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.208][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:31.209][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:31.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.210][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:31.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:31.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.222][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.226][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.229][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.232][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.233][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.234][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.235][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.246][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:31.247][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:31.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.249][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.253][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.254][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:31.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.260][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:31.265][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:31.266][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:31.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:31.267][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 15:01:31.275][biodb::testThat]
biodb.INFO [2024-03-02 15:01:31.276][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-02 15:01:31.276][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:31.277][biodb::testThat]
biodb.DEBUG[2024-03-02 15:01:31.279][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-03-02 15:01:31.286][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-02 15:01:31.290][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-03-02 15:01:31.291][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-03-02 15:01:31.292][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-02 15:01:31.293][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-02 15:01:31.294][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-03-02 15:01:31.295][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-03-02 15:01:31.296][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-02 15:01:31.297][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-02 15:01:31.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:31.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:31.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:31.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:31.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:31.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:31.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:31.311][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-03-02 15:01:31.327][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 15:01:31.328][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 15:01:31.329][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-03-02 15:01:32.535][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-03-02 15:01:33.276][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 15:01:33.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-03-02 15:01:33.298][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-03-02 15:01:33.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:33.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:33.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:33.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:33.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:33.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:33.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:33.327][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-03-02 15:01:33.338][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 15:01:33.339][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 15:01:33.351][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-03-02 15:01:33.947][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-03-02 15:01:34.526][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-02 15:01:34.529][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-03-02 15:01:34.534][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-03-02 15:01:34.536][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-03-02 15:01:34.538][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-02 15:01:34.539][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-03-02 15:01:34.540][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-03-02 15:01:34.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:34.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:34.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:34.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:34.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:34.549][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:34.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 15:01:34.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.556][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:34.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:34.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.562][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-03-02 15:01:34.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:34.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.582][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.585][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.592][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:34.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-02 15:01:34.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:34.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:34.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:34.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:34.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:34.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-02 15:01:34.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.630][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:34.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-03-02 15:01:34.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.637][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-03-02 15:01:34.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-03-02 15:01:34.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.641][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.644][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.650][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-03-02 15:01:34.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-02 15:01:34.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-02 15:01:34.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:34.683][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-03-02 15:01:34.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-02 15:01:34.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-02 15:01:34.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-02 15:01:34.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-02 15:01:34.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-02 15:01:34.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-02 15:01:34.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-02 15:01:34.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-02 15:01:34.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-02 15:01:34.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-02 15:01:34.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-02 15:01:34.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-02 15:01:34.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 15:01:34.716][biodb::testThat]
biodb.INFO [2024-03-02 15:01:34.717][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-02 15:01:34.717][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:34.718][biodb::testThat]
biodb.TRACE[2024-03-02 15:01:34.721][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.722][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.723][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:34.724][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-03-02 15:01:34.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:34.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:34.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:34.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:34.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:34.761][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-03-02 15:01:34.763][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-03-02 15:01:34.765][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-02 15:01:34.766][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-02 15:01:34.767][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-03-02 15:01:35.412][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-03-02 15:01:36.026][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-02 15:01:36.028][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-03-02 15:01:36.032][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-03-02 15:01:36.044][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-03-02 15:01:36.060][biodb::testThat]
biodb.INFO [2024-03-02 15:01:36.061][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-03-02 15:01:36.062][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:36.063][biodb::testThat]
biodb.TRACE[2024-03-02 15:01:36.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:36.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:36.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:36.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:36.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:36.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:36.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-02 15:01:36.120][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-03-02 15:01:36.123][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-02 15:01:36.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-03-02 15:01:36.137][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-02 15:01:36.138][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-03-02 15:01:36.155][biodb::testThat]
biodb.INFO [2024-03-02 15:01:36.156][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-03-02 15:01:36.156][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:36.157][biodb::testThat]
biodb.TRACE[2024-03-02 15:01:36.167][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:36.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:36.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.170][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:36.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:36.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.173][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:36.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:36.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.176][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:36.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:36.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.209][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:36.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:36.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.213][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-02 15:01:36.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-02 15:01:36.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.216][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:36.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-02 15:01:36.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:36.220][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:36.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-02 15:01:36.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:36.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-02 15:01:36.229][biodb::testThat]
biodb.INFO [2024-03-02 15:01:36.230][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-02 15:01:36.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:36.232][biodb::testThat]
biodb.INFO [2024-03-02 15:01:36.240][biodb::testThat]
biodb.INFO [2024-03-02 15:01:36.241][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-02 15:01:36.242][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:36.243][biodb::testThat]
biodb.INFO [2024-03-02 15:01:36.250][biodb::testThat]
biodb.INFO [2024-03-02 15:01:36.251][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-02 15:01:36.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:36.253][biodb::testThat]
biodb.DEBUG[2024-03-02 15:01:36.265][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-03-02 15:01:36.932][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-03-02 15:01:37.596][biodb::testThat]
biodb.INFO [2024-03-02 15:01:37.597][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-02 15:01:37.597][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-02 15:01:37.598][biodb::testThat]
biodb.DEBUG[2024-03-02 15:01:42.161][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-03-02 15:01:42.454][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:42.455][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:42.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:42.457][ef$get] fields variable is a list.
biodb.TRACE[2024-03-02 15:01:42.458][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-02 15:01:42.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-02 15:01:42.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-02 15:01:42.460][ef$get] fields variable is a list.
biodb.INFO [2024-03-02 15:01:42.461][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 15:01:42.462][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-03-02 15:01:42.463][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-03-02 15:01:42.463][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 15:01:42.464][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.465][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.467][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-02 15:01:42.475][biodb::testContext]
biodb.INFO [2024-03-02 15:01:42.476][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 15:01:42.477][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-03-02 15:01:42.478][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-02 15:01:42.478][biodb::testContext]
biodb.INFO [2024-03-02 15:01:42.480][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-02 15:01:42.481][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-02 15:01:42.485][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:42.485][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-02 15:01:42.486][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-02 15:01:42.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.489][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-02 15:01:42.490][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-02 15:01:42.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.493][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-02 15:01:42.494][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-02 15:01:42.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.497][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-02 15:01:42.498][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-02 15:01:42.498][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-02 15:01:42.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.501][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-02 15:01:42.502][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-02 15:01:42.503][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-02 15:01:42.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.506][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-02 15:01:42.507][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-02 15:01:42.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.509][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-02 15:01:42.510][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-02 15:01:42.521][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-02 15:01:42.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.524][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-02 15:01:42.524][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-02 15:01:42.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.527][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-02 15:01:42.528][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-02 15:01:42.529][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-02 15:01:42.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.532][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-02 15:01:42.533][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-02 15:01:42.534][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-02 15:01:42.535][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-02 15:01:42.535][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-02 15:01:42.536][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-02 15:01:42.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.539][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-02 15:01:42.540][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-02 15:01:42.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.543][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-02 15:01:42.544][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-02 15:01:42.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.547][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-02 15:01:42.548][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-02 15:01:42.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.550][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-02 15:01:42.551][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-02 15:01:42.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.554][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-02 15:01:42.555][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-02 15:01:42.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.558][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-02 15:01:42.559][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-02 15:01:42.577][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-02 15:01:42.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.580][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-02 15:01:42.581][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-02 15:01:42.582][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-02 15:01:42.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.584][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[2024-03-02 15:01:42.585][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-02 15:01:42.586][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.587][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-02 15:01:42.588][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.589][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:42.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.590][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.591][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.592][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.593][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 15:01:42.594][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:42.595][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.595][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-02 15:01:42.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:42.597][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.599][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:42.599][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 15:01:42.599][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 15:01:42.599][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 15:01:42.599][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 15:01:42.600][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:42.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.602][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:42.603][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.604][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.604][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.605][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.606][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:42.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:42.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.609][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.610][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-02 15:01:42.611][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.612][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 15:01:42.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.613][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:42.614][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.615][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.616][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.617][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.618][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 15:01:42.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:42.619][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.620][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-02 15:01:42.621][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:42.622][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.622][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.623][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:42.623][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-02 15:01:42.623][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-02 15:01:42.623][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-02 15:01:42.623][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-02 15:01:42.624][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:42.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:42.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.629][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.630][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:42.631][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:42.632][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.632][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.633][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-02 15:01:42.635][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.635][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-02 15:01:42.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:42.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.639][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.640][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.641][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-02 15:01:42.642][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:42.643][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.643][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-02 15:01:42.644][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:42.645][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.646][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.647][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.647][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:42.648][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.650][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:42.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.652][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.653][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.654][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:42.654][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:42.655][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.656][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.657][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-02 15:01:42.658][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.659][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-02 15:01:42.660][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.661][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:42.662][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.662][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.663][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.664][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.665][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-02 15:01:42.666][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:42.667][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.667][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-02 15:01:42.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:42.669][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.670][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.671][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.671][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-02 15:01:42.672][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.674][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:42.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.680][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.681][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.682][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:42.683][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:42.683][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.684][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.685][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:42.686][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.749][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-02 15:01:42.750][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-02 15:01:42.751][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-02 15:01:42.753][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-02 15:01:42.754][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-02 15:01:42.755][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-02 15:01:42.756][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-02 15:01:42.757][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-02 15:01:42.758][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 15:01:42.759][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-02 15:01:42.760][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-02 15:01:42.761][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-02 15:01:42.763][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-02 15:01:42.764][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-02 15:01:42.765][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-02 15:01:42.766][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-02 15:01:42.767][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-02 15:01:42.768][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-02 15:01:42.769][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-02 15:01:42.770][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-02 15:01:42.771][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-02 15:01:42.772][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-02 15:01:42.774][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-02 15:01:42.775][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-02 15:01:42.776][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-02 15:01:42.777][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-02 15:01:42.778][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-02 15:01:42.779][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-02 15:01:42.780][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-02 15:01:42.781][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-02 15:01:42.782][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-02 15:01:42.784][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-02 15:01:42.785][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-02 15:01:42.786][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-02 15:01:42.787][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-02 15:01:42.788][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-02 15:01:42.789][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-02 15:01:42.790][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-02 15:01:42.791][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-02 15:01:42.792][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-02 15:01:42.793][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-02 15:01:42.795][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-02 15:01:42.796][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-02 15:01:42.797][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-02 15:01:42.798][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-02 15:01:42.799][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-02 15:01:42.800][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-02 15:01:42.801][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-02 15:01:42.802][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-02 15:01:42.803][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-02 15:01:42.805][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-02 15:01:42.806][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-02 15:01:42.807][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-02 15:01:42.808][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-02 15:01:42.809][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-02 15:01:42.810][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-02 15:01:42.811][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-02 15:01:42.816][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-02 15:01:42.817][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-02 15:01:42.818][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-02 15:01:42.820][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-02 15:01:42.821][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-02 15:01:42.822][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-02 15:01:42.823][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-02 15:01:42.824][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-02 15:01:42.825][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-02 15:01:42.826][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-02 15:01:42.827][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-02 15:01:42.828][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-02 15:01:42.829][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-02 15:01:42.831][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-02 15:01:42.832][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-02 15:01:42.833][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-02 15:01:42.834][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-02 15:01:42.835][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-02 15:01:42.836][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-02 15:01:42.837][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-02 15:01:42.838][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-02 15:01:42.840][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-02 15:01:42.841][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-02 15:01:42.842][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-02 15:01:42.843][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-02 15:01:42.844][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-02 15:01:42.845][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-02 15:01:42.846][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-02 15:01:42.847][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-02 15:01:42.848][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.849][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-02 15:01:42.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-02 15:01:42.938][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-03-02 15:01:42.939][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-03-02 15:01:42.940][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.941][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-03-02 15:01:42.942][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.943][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-02 15:01:42.944][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.945][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.945][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.946][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.947][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-03-02 15:01:42.948][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-02 15:01:42.949][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.950][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-03-02 15:01:42.950][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-02 15:01:42.955][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-03-02 15:01:42.955][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-03-02 15:01:42.955][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-03-02 15:01:42.955][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-03-02 15:01:42.956][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-02 15:01:42.957][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-02 15:01:42.958][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-02 15:01:42.959][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-02 15:01:42.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-02 15:01:42.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-02 15:01:42.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-02 15:01:42.963][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-03-02 15:01:42.964][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-02 15:01:42.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-02 15:01:42.966][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-02 15:01:42.966][self$setPropertyValue]
biodb.DEBUG[2024-03-02 15:01:42.968][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-02 15:01:42.970][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-03-02 15:01:42.971][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-03-02 15:01:42.972][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-03-02 15:01:42.973][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-03-02 15:01:42.974][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 15:01:42.975][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-02 15:01:42.976][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-03-02 15:01:42.977][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-02 15:01:42.978][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-03-02 15:01:42.979][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-03-02 15:01:42.979][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-02 15:01:42.980][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-02 15:01:42.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-02 15:01:42.981][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-02 15:01:42.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-02 15:01:42.983][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-02 15:01:42.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
  4.058   0.309  14.743

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 ‘1.6.0’
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log’
for details.

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package ‘biodbExpasy’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)