Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/33HostnameOS / ArchCHECK
biodbExpasy 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-22 09:55 -0400 (Sat, 22 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_19
git_last_commit: de004e8
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.4 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on nebbiolo1

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

raw results


Summary

Package: biodbExpasy
Version: 1.8.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
StartedAt: 2024-06-22 16:01:54 -0400 (Sat, 22 Jun 2024)
EndedAt: 2024-06-22 16:02:39 -0400 (Sat, 22 Jun 2024)
EllapsedTime: 45.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-06-22 16:02:30.603][biodb::testContext]
biodb.INFO [2024-06-22 16:02:30.605][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:02:30.606][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-22 16:02:30.607][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:02:30.608][biodb::testContext]
biodb.INFO [2024-06-22 16:02:30.615][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:02:30.617][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:02:30.625][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:30.626][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:02:30.627][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:02:30.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.631][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:02:30.651][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:02:30.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.655][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:02:30.656][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:02:30.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.660][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:02:30.661][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:02:30.662][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:02:30.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.665][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:02:30.666][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:02:30.667][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:02:30.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.671][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:02:30.672][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:02:30.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.676][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:02:30.677][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:02:30.678][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:02:30.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.682][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:02:30.683][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:02:30.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.687][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:02:30.688][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:02:30.689][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:02:30.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.692][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:02:30.693][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:02:30.694][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:02:30.695][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:02:30.696][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:02:30.697][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:02:30.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.701][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:02:30.702][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:02:30.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.706][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:02:30.707][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:02:30.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.711][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:02:30.712][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:02:30.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.716][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:02:30.717][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:02:30.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.720][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:02:30.721][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:02:30.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.725][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:02:30.726][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:02:30.730][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:02:30.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.734][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:02:30.735][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:02:30.736][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:02:30.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.743][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:02:30.779][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.801][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-22 16:02:30.802][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.803][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:30.804][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.805][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.806][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.806][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.807][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:02:30.808][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:30.809][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.810][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:02:30.811][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:30.812][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.813][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.814][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:30.814][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:02:30.814][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:02:30.814][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:02:30.814][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:02:30.815][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:30.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:30.816][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:30.817][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:30.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:30.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:30.820][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.821][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.821][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:30.822][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:30.823][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.824][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.825][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:02:30.827][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.828][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:02:30.829][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:30.830][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.831][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.832][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.833][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.834][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:02:30.835][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:30.836][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.837][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:02:30.838][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:30.838][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.839][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.840][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:30.840][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:02:30.840][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:02:30.840][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:02:30.840][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:02:30.841][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:30.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:30.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:30.844][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:30.845][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:30.845][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:30.846][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.847][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.848][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:30.849][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:30.850][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.851][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.852][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:02:30.853][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.854][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-22 16:02:30.855][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.856][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:30.857][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.858][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.859][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.859][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.860][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:02:30.861][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:30.862][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.863][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:02:30.864][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:30.865][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.866][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.867][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.868][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:30.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:30.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:30.870][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:30.871][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:30.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:30.873][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.874][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.874][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:30.875][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:30.876][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.877][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.878][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:02:30.880][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.880][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:02:30.881][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.882][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:30.883][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.884][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.885][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.886][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.887][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:02:30.888][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:30.889][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.889][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:02:30.890][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:30.891][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.892][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:30.893][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.894][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:30.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:30.896][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:30.896][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:30.897][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:30.898][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:30.899][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:30.900][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.901][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:30.902][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:30.902][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:30.903][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:30.907][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:30.908][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.913][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[2024-06-22 16:02:30.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.933][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[2024-06-22 16:02:30.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.938][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[2024-06-22 16:02:30.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:30.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:30.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:30.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:30.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:30.988][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:02:30.993][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:02:30.995][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:02:30.996][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:02:30.998][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:02:30.999][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:02:31.000][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:02:31.002][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:02:31.003][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:02:31.004][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:02:31.006][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:02:31.007][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:02:31.009][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:02:31.010][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:02:31.011][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:02:31.013][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:02:31.014][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:02:31.015][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:02:31.017][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:02:31.018][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:02:31.019][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:02:31.021][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:02:31.022][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:02:31.024][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:02:31.025][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:02:31.026][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:02:31.028][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:02:31.029][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:02:31.030][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:02:31.032][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:02:31.033][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:02:31.034][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:02:31.036][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:02:31.037][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:02:31.039][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:02:31.040][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:02:31.041][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:02:31.055][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:02:31.056][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:02:31.058][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:02:31.059][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:02:31.060][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:02:31.062][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:02:31.063][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:02:31.065][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:02:31.066][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:02:31.067][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:02:31.069][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:02:31.070][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:02:31.072][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:02:31.073][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:02:31.074][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:02:31.076][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:02:31.077][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:02:31.078][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:02:31.080][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:02:31.081][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:02:31.083][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:02:31.084][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:02:31.085][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:02:31.087][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:02:31.088][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:02:31.090][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:02:31.091][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:02:31.092][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:02:31.094][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:02:31.095][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:02:31.096][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:02:31.098][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:02:31.099][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:02:31.101][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:02:31.102][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:02:31.103][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:02:31.105][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:02:31.106][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:02:31.107][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:02:31.109][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:02:31.110][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:02:31.111][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:02:31.113][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:02:31.114][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:02:31.115][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:02:31.117][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:02:31.123][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:02:31.124][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:02:31.128][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:31.129][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.130][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.131][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[2024-06-22 16:02:31.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.141][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[2024-06-22 16:02:31.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.177][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[2024-06-22 16:02:31.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:31.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:31.236][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-22 16:02:31.245][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:31.247][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:31.248][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-22 16:02:31.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:31.249][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:31.250][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:31.251][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:31.252][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:31.253][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:31.254][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-22 16:02:31.255][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:31.256][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:31.257][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-22 16:02:31.258][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:31.259][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-22 16:02:31.259][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:31.259][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:31.259][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:31.260][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:31.260][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:31.261][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:02:31.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:31.263][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:31.264][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:31.265][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:31.266][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:31.266][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:31.267][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:02:31.268][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:31.269][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:31.270][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:31.271][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:31.276][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:02:31.303][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:31.304][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-22 16:02:31.308][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:31.312][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-22 16:02:31.316][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:02:31.317][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:02:31.318][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-22 16:02:31.327][biodb::testThat]
biodb.INFO [2024-06-22 16:02:31.328][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-22 16:02:31.329][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:31.329][biodb::testThat]
biodb.TRACE[2024-06-22 16:02:31.333][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-22 16:02:31.334][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:02:31.338][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:02:31.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:31.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.359][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.361][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:02:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.399][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.414][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.422][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:31.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.425][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.429][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.433][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.436][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:31.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.502][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.506][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.513][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:31.546][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-22 16:02:31.549][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:31.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:31.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.552][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:31.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:31.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.556][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:31.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:31.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:31.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:31.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.621][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.625][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.629][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.649][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.650][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.651][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.652][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.674][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.675][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.677][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.688][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.692][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.699][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.700][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.702][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.703][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.713][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.716][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.720][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.724][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.725][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.727][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.727][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.760][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.761][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.762][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.766][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.767][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.769][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.773][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.774][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.776][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.779][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.780][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.782][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.797][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-22 16:02:31.828][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:02:31.830][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:02:31.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:31.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:31.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:31.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:31.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:31.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:31.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:02:31.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.845][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:31.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:31.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:31.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.853][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:31.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:31.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.857][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.860][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.868][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:31.893][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-22 16:02:31.912][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:31.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:31.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.916][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:31.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:31.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.919][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:31.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:31.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:31.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:31.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.934][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.969][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.972][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.976][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:31.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:31.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:31.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:31.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:31.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:32.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:32.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.004][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:32.005][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:32.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.007][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:32.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:32.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:32.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:32.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.021][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:32.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:32.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:32.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:32.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.029][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:32.030][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:32.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.031][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:32.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:32.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.042][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.046][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.049][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.053][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.054][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.055][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.056][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.066][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:32.067][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:32.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.069][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.072][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.073][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:32.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.075][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:32.079][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:32.080][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:32.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:32.081][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:02:32.087][biodb::testThat]
biodb.INFO [2024-06-22 16:02:32.088][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-22 16:02:32.089][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:32.090][biodb::testThat]
biodb.DEBUG[2024-06-22 16:02:32.092][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-22 16:02:32.099][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-22 16:02:32.103][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.TRACE[2024-06-22 16:02:32.104][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-22 16:02:32.105][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-22 16:02:32.106][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-22 16:02:32.107][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:02:32.108][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-22 16:02:32.109][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-22 16:02:32.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:32.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:32.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:32.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:32.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:32.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:32.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:32.123][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-22 16:02:32.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:02:32.142][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:02:32.143][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-22 16:02:32.856][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-22 16:02:33.532][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:02:33.537][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-22 16:02:33.568][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-22 16:02:33.572][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:33.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:33.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:33.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:33.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:33.585][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:33.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:33.612][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-22 16:02:33.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:02:33.628][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:02:33.642][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-22 16:02:34.124][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-22 16:02:34.588][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:02:34.592][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-22 16:02:34.599][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-22 16:02:34.605][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-06-22 16:02:34.608][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-22 16:02:34.610][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-22 16:02:34.613][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:02:34.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:34.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:34.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:34.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:34.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:34.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:34.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:02:34.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.646][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:34.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:34.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.658][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:34.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:34.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.684][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.688][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.695][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:34.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:34.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:34.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:34.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:34.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:34.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:34.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:02:34.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.723][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:34.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:34.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.730][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:34.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:34.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.734][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.738][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.745][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:34.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:34.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:34.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:34.781][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-22 16:02:34.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:02:34.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:02:34.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:02:34.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:02:34.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:02:34.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:02:34.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:02:34.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:02:34.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:02:34.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:02:34.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:02:34.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:02:34.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:02:34.818][biodb::testThat]
biodb.INFO [2024-06-22 16:02:34.819][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-22 16:02:34.820][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:34.821][biodb::testThat]
biodb.TRACE[2024-06-22 16:02:34.823][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.824][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.826][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:34.827][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-22 16:02:34.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:34.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:34.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:34.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:34.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:34.862][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:02:34.863][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:02:34.866][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:02:34.870][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:02:34.872][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-22 16:02:35.331][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-22 16:02:35.826][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:02:35.832][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-22 16:02:35.840][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-22 16:02:35.856][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-22 16:02:35.883][biodb::testThat]
biodb.INFO [2024-06-22 16:02:35.885][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-22 16:02:35.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:35.888][biodb::testThat]
biodb.TRACE[2024-06-22 16:02:35.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:35.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:35.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:35.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:35.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:35.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:35.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:35.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:35.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:35.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:35.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:35.956][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:02:35.958][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-22 16:02:35.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-22 16:02:35.989][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-22 16:02:35.990][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-22 16:02:36.005][biodb::testThat]
biodb.INFO [2024-06-22 16:02:36.006][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-22 16:02:36.007][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:36.008][biodb::testThat]
biodb.TRACE[2024-06-22 16:02:36.017][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:36.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:36.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:36.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:36.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:36.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:36.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:36.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:36.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:36.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:36.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:36.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:36.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:36.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:36.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:36.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:36.063][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:36.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:36.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:36.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:36.067][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:36.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:36.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:36.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:36.071][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:36.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:36.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:36.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:36.074][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:36.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:36.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:36.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:02:36.082][biodb::testThat]
biodb.INFO [2024-06-22 16:02:36.083][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-22 16:02:36.084][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:36.085][biodb::testThat]
biodb.INFO [2024-06-22 16:02:36.093][biodb::testThat]
biodb.INFO [2024-06-22 16:02:36.094][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-22 16:02:36.095][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:36.096][biodb::testThat]
biodb.INFO [2024-06-22 16:02:36.102][biodb::testThat]
biodb.INFO [2024-06-22 16:02:36.103][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-22 16:02:36.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:36.105][biodb::testThat]
biodb.DEBUG[2024-06-22 16:02:36.118][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-06-22 16:02:36.562][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-06-22 16:02:37.053][biodb::testThat]
biodb.INFO [2024-06-22 16:02:37.055][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-22 16:02:37.058][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:37.060][biodb::testThat]
biodb.DEBUG[2024-06-22 16:02:37.533][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-22 16:02:38.201][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:38.203][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:38.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:38.206][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:38.208][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:38.210][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:38.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:38.212][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:02:38.214][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:02:38.216][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-22 16:02:38.217][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-22 16:02:38.218][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:02:38.219][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.222][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.224][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-22 16:02:38.235][biodb::testContext]
biodb.INFO [2024-06-22 16:02:38.236][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:02:38.237][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-22 16:02:38.238][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:02:38.239][biodb::testContext]
biodb.INFO [2024-06-22 16:02:38.241][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:02:38.243][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:02:38.246][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:38.247][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:02:38.248][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:02:38.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.252][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:02:38.253][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:02:38.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.256][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:02:38.257][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:02:38.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.260][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:02:38.261][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:02:38.262][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:02:38.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.265][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[2024-06-22 16:02:38.265][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:02:38.266][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:02:38.267][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:02:38.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.271][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:02:38.272][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:02:38.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.275][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:02:38.276][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:02:38.277][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:02:38.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.280][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:02:38.281][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:02:38.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.284][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:02:38.285][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:02:38.286][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:02:38.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.290][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:02:38.291][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:02:38.291][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:02:38.292][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:02:38.293][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:02:38.294][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:02:38.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.298][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:02:38.298][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:02:38.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.302][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:02:38.303][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:02:38.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.306][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:02:38.307][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:02:38.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.310][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:02:38.311][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:02:38.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.315][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:02:38.316][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:02:38.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.319][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:02:38.320][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:02:38.323][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:02:38.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.327][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:02:38.328][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:02:38.329][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:02:38.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.332][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:02:38.334][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.335][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-22 16:02:38.336][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.337][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:38.337][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.338][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.339][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.340][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.341][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:02:38.342][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:38.343][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.344][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:02:38.345][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:38.346][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.347][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.348][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:38.348][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:02:38.348][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:02:38.348][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:02:38.348][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:02:38.349][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:38.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:38.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.355][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.356][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:38.356][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:38.357][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.358][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.359][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:02:38.361][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.362][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:02:38.363][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.364][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:38.365][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.366][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.366][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.367][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.368][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:02:38.369][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:38.370][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.371][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:02:38.372][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:38.373][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.374][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.375][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:38.375][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:02:38.375][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:02:38.375][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:02:38.375][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:02:38.380][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:38.381][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.383][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:38.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.387][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.387][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:38.388][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:38.389][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.390][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.391][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:02:38.393][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.394][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-22 16:02:38.395][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:38.396][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.397][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.398][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.399][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.400][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:02:38.401][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:38.402][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.403][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:02:38.404][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:38.405][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.406][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.407][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.408][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:38.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:38.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.413][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.414][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.414][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:38.415][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:38.416][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.417][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.418][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:02:38.420][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.421][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:02:38.422][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.422][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:38.423][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.424][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.425][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.427][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:02:38.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:38.429][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.430][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:02:38.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:38.432][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.432][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.433][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.434][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:38.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:38.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.439][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.440][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.441][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:38.442][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:38.443][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.444][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.445][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:38.446][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.499][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[2024-06-22 16:02:38.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.517][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:02:38.518][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:02:38.519][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:02:38.521][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:02:38.522][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:02:38.523][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:02:38.524][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:02:38.526][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:02:38.527][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:02:38.528][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:02:38.529][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:02:38.531][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:02:38.532][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:02:38.533][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:02:38.535][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:02:38.536][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:02:38.537][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:02:38.538][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:02:38.540][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:02:38.541][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:02:38.546][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:02:38.547][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:02:38.549][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:02:38.550][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:02:38.551][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:02:38.552][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:02:38.554][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:02:38.555][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:02:38.556][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:02:38.558][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:02:38.559][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:02:38.560][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:02:38.561][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:02:38.563][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:02:38.564][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:02:38.565][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:02:38.566][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:02:38.568][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:02:38.569][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:02:38.570][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:02:38.571][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:02:38.573][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:02:38.574][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:02:38.575][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:02:38.577][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:02:38.578][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:02:38.579][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:02:38.580][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:02:38.582][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:02:38.583][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:02:38.584][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:02:38.585][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:02:38.587][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:02:38.588][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:02:38.589][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:02:38.591][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:02:38.592][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:02:38.593][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:02:38.594][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:02:38.596][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:02:38.597][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:02:38.598][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:02:38.599][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:02:38.601][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:02:38.602][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:02:38.603][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:02:38.604][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:02:38.606][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:02:38.607][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:02:38.608][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:02:38.609][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:02:38.611][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:02:38.612][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:02:38.613][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:02:38.615][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:02:38.616][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:02:38.617][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:02:38.618][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:02:38.620][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:02:38.621][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:02:38.622][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:02:38.623][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:02:38.625][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:02:38.626][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:02:38.628][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:02:38.629][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:38.629][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.631][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:38.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:38.734][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-22 16:02:38.735][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:38.737][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.738][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-22 16:02:38.739][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.740][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:38.741][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.742][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.743][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.744][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.744][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-22 16:02:38.745][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:38.746][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.747][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-22 16:02:38.748][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:38.749][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-22 16:02:38.749][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:38.749][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:38.749][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:38.750][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:38.751][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:38.752][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:02:38.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.754][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.754][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:38.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:38.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:38.757][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:38.758][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:02:38.759][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:38.760][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:38.760][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:38.761][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:38.763][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:02:38.766][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:38.766][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-22 16:02:38.768][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:38.769][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-22 16:02:38.770][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:02:38.771][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:02:38.772][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-22 16:02:38.773][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:02:38.774][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-22 16:02:38.775][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-22 16:02:38.775][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:02:38.776][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:38.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:38.778][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:38.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:38.780][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:38.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

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

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbExpasy.Rcheck/00install.out

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