Back to Long Tests report for BioC 3.18

This page was generated on 2024-04-13 23:55:02 -0400 (Sat, 13 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4675
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4413
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4436
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: 2024-04-13 09:55:01 -0400 (Sat, 13 Apr 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 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbExpasy on merida1


To the developers/maintainers of the biodbExpasy package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: biodbExpasy
Version: 1.6.0
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: 2024-04-13 16:02:15 -0400 (Sat, 13 Apr 2024)
EndedAt: 2024-04-13 16:03:15 -0400 (Sat, 13 Apr 2024)
EllapsedTime: 59.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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.
Type 'q()' to quit R.

> # 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 [2024-04-13 16:03:00.430][biodb::testContext]
biodb.INFO [2024-04-13 16:03:00.434][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:03:00.436][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-04-13 16:03:00.437][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:03:00.438][biodb::testContext]
biodb.INFO [2024-04-13 16:03:00.446][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:03:00.449][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:03:00.458][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:03:00.459][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:03:00.461][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:03:00.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.466][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:03:00.494][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:03:00.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.499][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:03:00.501][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:03:00.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.506][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:03:00.507][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:03:00.509][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:03:00.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.514][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:03:00.515][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:03:00.517][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:03:00.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.522][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:03:00.523][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:03:00.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.527][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[2024-04-13 16:03:00.529][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:03:00.530][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:03:00.531][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:03:00.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.536][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:03:00.538][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:03:00.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.542][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[2024-04-13 16:03:00.543][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:03:00.544][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:03:00.546][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:03:00.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.551][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:03:00.552][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:03:00.554][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:03:00.555][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:03:00.557][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:03:00.558][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:03:00.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.563][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:03:00.565][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:03:00.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.570][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:03:00.571][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:03:00.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.576][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:03:00.578][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:03:00.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.583][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:03:00.584][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:03:00.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.589][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:03:00.591][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:03:00.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.596][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:03:00.597][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:03:00.608][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:03:00.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.613][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:03:00.615][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:03:00.616][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:03:00.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.625][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:03:00.675][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.699][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-13 16:03:00.701][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.702][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:00.704][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.705][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.707][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.708][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.709][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:03:00.711][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:00.712][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.714][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:03:00.715][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:00.717][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.718][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.719][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:03:00.719][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:03:00.719][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:03:00.719][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:03:00.719][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:03:00.721][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:03:00.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:00.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:00.725][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:00.726][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:00.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:00.729][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.730][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.737][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:00.739][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:00.740][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.741][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.742][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:03:00.744][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.745][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:03:00.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:00.749][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.750][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.751][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.752][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.753][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:03:00.755][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:00.756][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.757][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:03:00.758][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:00.759][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.760][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.761][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:03:00.761][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:03:00.761][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:03:00.761][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:03:00.761][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:03:00.763][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:03:00.764][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:00.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:00.766][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:00.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:00.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:00.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.770][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:00.773][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:00.774][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.775][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.776][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:03:00.778][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.779][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-13 16:03:00.781][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.782][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:00.783][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.784][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.785][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.786][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.787][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:03:00.789][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:00.790][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.791][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:03:00.792][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:00.793][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.794][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.796][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.797][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:03:00.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:00.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:00.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:00.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:00.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:00.803][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.805][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.806][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:00.807][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:00.808][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.809][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.811][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:03:00.813][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.814][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:03:00.815][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.816][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:00.817][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.819][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.820][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.821][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.822][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:03:00.823][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:00.824][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.826][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:03:00.827][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:00.828][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.829][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:00.830][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.831][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:03:00.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:00.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:00.835][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:00.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:00.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:00.838][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:00.839][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.841][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:00.842][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:00.843][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:00.844][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:00.848][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:03:00.849][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.850][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[2024-04-13 16:03:00.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:00.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:00.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:00.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:00.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:00.940][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:03:00.945][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:03:00.946][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:03:00.948][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:03:00.950][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:03:00.951][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:03:00.953][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:03:00.954][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:03:00.956][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:03:00.958][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:03:00.959][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:03:00.961][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:03:00.963][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:03:00.964][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:03:00.966][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:03:00.967][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:03:00.969][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:03:00.971][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:03:00.972][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:03:00.974][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:03:00.975][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:03:00.977][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:03:00.979][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:03:00.980][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:03:00.982][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:03:00.984][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:03:00.985][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:03:00.987][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:03:00.988][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:03:00.990][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:03:00.992][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:03:00.993][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:03:00.995][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:03:00.997][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:03:00.998][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:03:01.000][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:03:01.001][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:03:01.003][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:03:01.005][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:03:01.006][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:03:01.008][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:03:01.010][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:03:01.011][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:03:01.013][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:03:01.015][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:03:01.016][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:03:01.018][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:03:01.020][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:03:01.021][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:03:01.023][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:03:01.024][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:03:01.026][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:03:01.028][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:03:01.029][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:03:01.031][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:03:01.032][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:03:01.034][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:03:01.036][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:03:01.037][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:03:01.039][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:03:01.041][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:03:01.043][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:03:01.045][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:03:01.047][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:03:01.049][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:03:01.055][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:03:01.057][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:03:01.059][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:03:01.060][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:03:01.062][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:03:01.063][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:03:01.065][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:03:01.067][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:03:01.068][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:03:01.070][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:03:01.071][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:03:01.073][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:03:01.074][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:03:01.076][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:03:01.078][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:03:01.079][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:03:01.081][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:03:01.082][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:03:01.089][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:03:01.091][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:03:01.095][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:03:01.096][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.098][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:01.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:01.230][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-04-13 16:03:01.241][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:03:01.243][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:01.245][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-04-13 16:03:01.246][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:01.247][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:01.248][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:01.249][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:01.250][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:01.251][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:01.253][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-04-13 16:03:01.254][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:01.255][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:01.256][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-04-13 16:03:01.257][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:01.258][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-04-13 16:03:01.258][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:03:01.258][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:03:01.258][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:03:01.260][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:01.261][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:03:01.262][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:03:01.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:01.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:01.265][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:01.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:01.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:01.269][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:01.270][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:03:01.271][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:01.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:01.273][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:01.274][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:01.281][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:03:01.306][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:03:01.307][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-04-13 16:03:01.312][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:03:01.316][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-04-13 16:03:01.321][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:03:01.322][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:03:01.323][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-04-13 16:03:01.335][biodb::testThat]
biodb.INFO [2024-04-13 16:03:01.336][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-04-13 16:03:01.337][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:01.338][biodb::testThat]
biodb.TRACE[2024-04-13 16:03:01.342][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[2024-04-13 16:03:01.344][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:03:01.348][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:03:01.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:03:01.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:01.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:01.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:01.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:01.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:01.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:03:01.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.435][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.455][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.464][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:03:01.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.469][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.474][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.478][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.483][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:03:01.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.573][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.578][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.587][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:03:01.620][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-04-13 16:03:01.623][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:03:01.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:03:01.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.628][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:03:01.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:03:01.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.633][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:03:01.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:03:01.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.637][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:03:01.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:03:01.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.686][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.727][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.732][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.737][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:01.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.765][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.767][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.769][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.799][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.801][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.803][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.804][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.818][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.823][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.828][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.833][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.834][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.837][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.838][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.852][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.857][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.862][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.867][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.868][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.870][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.872][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.886][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:01.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:01.889][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.890][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.896][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.897][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:01.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.899][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.905][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.907][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:01.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.909][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.915][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:01.916][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:01.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:01.918][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:01.939][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[2024-04-13 16:03:02.002][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:03:02.004][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:03:02.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:03:02.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:02.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:02.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:02.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:02.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:02.016][FUN] Functions in observer BiodbConfig: [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[2024-04-13 16:03:02.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.024][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:02.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:02.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.033][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:03:02.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:02.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.038][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.043][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.052][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:03:02.085][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-04-13 16:03:02.110][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:03:02.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:03:02.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.115][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:03:02.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:03:02.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.120][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:03:02.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:03:02.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.124][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:03:02.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:03:02.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.139][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.179][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.183][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.188][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:02.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.227][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.228][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.235][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:02.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:02.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:02.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:02.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:02.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:02.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.265][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:02.267][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:02.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.269][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:02.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:02.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.285][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.290][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.294][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.299][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.301][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.303][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.304][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.318][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:02.320][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:02.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.322][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.328][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.330][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:02.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.332][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:02.338][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:02.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:02.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:02.342][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:03:02.352][biodb::testThat]
biodb.INFO [2024-04-13 16:03:02.353][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-13 16:03:02.354][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:02.355][biodb::testThat]
biodb.DEBUG[2024-04-13 16:03:02.358][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-04-13 16:03:02.366][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-13 16:03:02.370][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-04-13 16:03:02.373][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-04-13 16:03:02.374][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-04-13 16:03:02.376][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-13 16:03:02.377][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-04-13 16:03:02.378][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:03:02.379][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-13 16:03:02.380][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-13 16:03:02.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:03:02.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:02.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:02.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:02.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:02.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:02.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:02.399][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-04-13 16:03:02.425][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-13 16:03:02.426][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-13 16:03:02.428][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-04-13 16:03:06.441][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-04-13 16:03:07.077][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-13 16:03:07.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-04-13 16:03:07.118][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-04-13 16:03:07.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:03:07.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:07.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:07.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:07.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:07.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:07.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:07.157][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-04-13 16:03:07.177][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-13 16:03:07.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-13 16:03:07.197][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-04-13 16:03:07.829][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-04-13 16:03:08.502][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-13 16:03:08.504][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-04-13 16:03:08.508][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-04-13 16:03:08.511][private$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[2024-04-13 16:03:08.513][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-13 16:03:08.515][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-04-13 16:03:08.516][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-04-13 16:03:08.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:03:08.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:08.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:08.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:08.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:08.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:08.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:03:08.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.537][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:08.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.547][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:03:08.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:08.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.576][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.580][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.600][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:03:08.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:03:08.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:08.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:08.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:08.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:08.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:08.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:03:08.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.638][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:08.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-04-13 16:03:08.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.647][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-04-13 16:03:08.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-04-13 16:03:08.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.652][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.657][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-04-13 16:03:08.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:03:08.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:03:08.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:03:08.714][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-04-13 16:03:08.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:03:08.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:03:08.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:03:08.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:03:08.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:03:08.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:03:08.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:03:08.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:03:08.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:03:08.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:03:08.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:03:08.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:03:08.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:03:08.757][biodb::testThat]
biodb.INFO [2024-04-13 16:03:08.759][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-13 16:03:08.760][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:08.761][biodb::testThat]
biodb.TRACE[2024-04-13 16:03:08.764][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.766][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.768][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:03:08.769][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-04-13 16:03:08.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:08.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:08.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:08.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:08.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:03:08.818][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:03:08.820][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:03:08.823][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-13 16:03:08.825][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-13 16:03:08.826][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-04-13 16:03:09.579][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-04-13 16:03:10.260][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-13 16:03:10.263][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-04-13 16:03:10.315][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-04-13 16:03:10.352][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-04-13 16:03:10.370][biodb::testThat]
biodb.INFO [2024-04-13 16:03:10.372][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-04-13 16:03:10.373][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:10.374][biodb::testThat]
biodb.TRACE[2024-04-13 16:03:10.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:10.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:10.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:10.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:10.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:10.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:10.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:03:10.450][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-04-13 16:03:10.453][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-13 16:03:10.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-04-13 16:03:10.474][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-13 16:03:10.476][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-04-13 16:03:10.496][biodb::testThat]
biodb.INFO [2024-04-13 16:03:10.498][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-04-13 16:03:10.499][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:10.500][biodb::testThat]
biodb.TRACE[2024-04-13 16:03:10.512][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:03:10.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:03:10.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.517][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:03:10.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:03:10.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:03:10.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:03:10.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.526][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:03:10.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:03:10.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.571][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:03:10.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:03:10.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.581][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:03:10.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:03:10.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.585][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:03:10.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:03:10.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:10.590][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:03:10.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:03:10.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:10.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:03:10.618][biodb::testThat]
biodb.INFO [2024-04-13 16:03:10.619][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-13 16:03:10.620][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:10.621][biodb::testThat]
biodb.INFO [2024-04-13 16:03:10.632][biodb::testThat]
biodb.INFO [2024-04-13 16:03:10.633][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-13 16:03:10.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:10.636][biodb::testThat]
biodb.INFO [2024-04-13 16:03:10.645][biodb::testThat]
biodb.INFO [2024-04-13 16:03:10.647][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-13 16:03:10.648][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:10.649][biodb::testThat]
biodb.DEBUG[2024-04-13 16:03:10.666][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[2024-04-13 16:03:11.368][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 [2024-04-13 16:03:12.083][biodb::testThat]
biodb.INFO [2024-04-13 16:03:12.084][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-13 16:03:12.085][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:03:12.086][biodb::testThat]
biodb.DEBUG[2024-04-13 16:03:13.592][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-04-13 16:03:13.942][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:13.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:13.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:13.946][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:03:13.947][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:03:13.948][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:03:13.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:03:13.950][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:03:13.952][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:03:13.953][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-04-13 16:03:13.954][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-04-13 16:03:13.955][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:03:13.956][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:13.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:13.958][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:13.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:13.960][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:13.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-13 16:03:13.973][biodb::testContext]
biodb.INFO [2024-04-13 16:03:13.974][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:03:13.975][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-04-13 16:03:13.976][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:03:13.977][biodb::testContext]
biodb.INFO [2024-04-13 16:03:13.980][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:03:13.981][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:03:13.986][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:03:13.987][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:03:13.988][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:03:13.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:13.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:13.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:13.992][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:03:13.994][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:03:13.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:13.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:13.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:13.998][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:03:13.999][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:03:14.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.002][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[2024-04-13 16:03:14.003][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:03:14.004][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:03:14.006][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:03:14.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.010][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:03:14.011][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:03:14.012][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:03:14.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.015][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[2024-04-13 16:03:14.016][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:03:14.018][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:03:14.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.022][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:03:14.023][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:03:14.024][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:03:14.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.028][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:03:14.029][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:03:14.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.034][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:03:14.035][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:03:14.036][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:03:14.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.040][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:03:14.041][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:03:14.043][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:03:14.044][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:03:14.045][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:03:14.046][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:03:14.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.050][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:03:14.051][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:03:14.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.056][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:03:14.057][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:03:14.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.061][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:03:14.062][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:03:14.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.066][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:03:14.068][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:03:14.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.072][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:03:14.073][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:03:14.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.088][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:03:14.089][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:03:14.099][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:03:14.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.103][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:03:14.104][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:03:14.106][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:03:14.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.110][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:03:14.112][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.113][self$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[2024-04-13 16:03:14.114][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.115][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:14.117][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.118][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.119][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.120][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.121][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:03:14.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:14.124][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.125][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:03:14.126][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:14.127][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.128][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.129][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:03:14.129][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:03:14.129][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:03:14.129][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:03:14.129][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:03:14.131][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:03:14.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.134][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:14.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.136][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.137][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.139][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.140][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:14.141][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:14.142][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.143][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.144][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:03:14.147][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.148][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:03:14.149][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.150][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:14.151][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.153][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.154][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.155][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.156][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:03:14.157][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:14.158][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.160][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:03:14.161][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:14.162][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.163][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.164][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:03:14.164][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:03:14.164][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:03:14.164][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:03:14.164][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:03:14.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:03:14.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.169][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:14.170][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.172][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.173][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.174][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:14.175][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:14.176][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.177][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.179][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:03:14.181][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.182][self$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[2024-04-13 16:03:14.183][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.184][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:14.185][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.187][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.188][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.190][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:03:14.191][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:14.192][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.194][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:03:14.195][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:14.196][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.197][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.198][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.199][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:03:14.200][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.203][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:14.204][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.205][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.206][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.207][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.208][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:14.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:14.210][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.211][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.213][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:03:14.215][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.216][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:03:14.217][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.218][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:14.219][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.221][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.222][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.223][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.224][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:03:14.225][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:14.226][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.227][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:03:14.229][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:14.230][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.231][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.232][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.233][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:03:14.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.236][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:14.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.240][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.241][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.242][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:14.243][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:14.244][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.245][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.247][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:03:14.248][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.344][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:03:14.345][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:03:14.347][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:03:14.348][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:03:14.350][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:03:14.352][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:03:14.353][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:03:14.355][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:03:14.356][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:03:14.358][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:03:14.360][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:03:14.361][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:03:14.363][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:03:14.365][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:03:14.366][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:03:14.368][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:03:14.369][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:03:14.371][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:03:14.373][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:03:14.374][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:03:14.376][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:03:14.378][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:03:14.379][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:03:14.381][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:03:14.383][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:03:14.384][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:03:14.386][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:03:14.388][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:03:14.389][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:03:14.391][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:03:14.392][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:03:14.394][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:03:14.396][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:03:14.397][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:03:14.399][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:03:14.400][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:03:14.402][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:03:14.404][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:03:14.405][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:03:14.407][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:03:14.408][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:03:14.410][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:03:14.412][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:03:14.413][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:03:14.415][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:03:14.416][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:03:14.418][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:03:14.420][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:03:14.421][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:03:14.423][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:03:14.425][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:03:14.426][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:03:14.428][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:03:14.429][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:03:14.431][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:03:14.433][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:03:14.434][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:03:14.436][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:03:14.437][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:03:14.439][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:03:14.440][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:03:14.442][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:03:14.444][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:03:14.445][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:03:14.447][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:03:14.448][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:03:14.450][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:03:14.452][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:03:14.453][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:03:14.455][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:03:14.456][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:03:14.458][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:03:14.460][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:03:14.461][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:03:14.463][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:03:14.465][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:03:14.466][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:03:14.468][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:03:14.469][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:03:14.471][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:03:14.473][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:03:14.474][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:03:14.476][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:03:14.477][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:03:14.479][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:03:14.480][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:03:14.481][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.483][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.492][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[2024-04-13 16:03:14.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.584][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[2024-04-13 16:03:14.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:03:14.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:03:14.616][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.18-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-04-13 16:03:14.618][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:03:14.620][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.621][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-04-13 16:03:14.622][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.623][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:03:14.625][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.626][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.627][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.628][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.629][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-04-13 16:03:14.631][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:03:14.632][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.633][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-04-13 16:03:14.634][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:03:14.635][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-04-13 16:03:14.635][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:03:14.635][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:03:14.635][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-04-13 16:03:14.637][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:03:14.638][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:03:14.639][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:03:14.640][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.642][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:03:14.644][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:03:14.645][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:03:14.646][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:03:14.647][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-04-13 16:03:14.648][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:03:14.649][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:03:14.650][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:03:14.652][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:03:14.653][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:03:14.657][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:03:14.658][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-04-13 16:03:14.659][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-04-13 16:03:14.661][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-04-13 16:03:14.663][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:03:14.664][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:03:14.665][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-04-13 16:03:14.666][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:03:14.668][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-04-13 16:03:14.669][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-04-13 16:03:14.670][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:03:14.671][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:03:14.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:03:14.673][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:03:14.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:03:14.675][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:03:14.676][FUN] Functions in observer 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 
  5.710   0.358  16.498

'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 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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)