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 palomino3

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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --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 16:07:44 -0400 (Sat, 22 Jun 2024)
EndedAt: 2024-06-22 16:14:39 -0400 (Sat, 22 Jun 2024)
EllapsedTime: 415.4 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 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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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 16:14:30.550][biodb::testContext]
biodb.INFO [2024-06-22 16:14:30.564][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:14:30.565][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-22 16:14:30.567][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:14:30.568][biodb::testContext]
biodb.INFO [2024-06-22 16:14:30.576][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:14:30.579][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:14:30.589][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:14:30.591][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:14:30.592][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:14:30.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.597][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:14:30.628][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:14:30.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.632][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 16:14:30.633][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:14:30.634][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:14:30.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.639][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:14:30.640][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:14:30.641][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:14:30.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.646][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:14:30.647][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:14:30.648][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:14:30.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.653][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:14:30.654][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:14:30.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.659][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:14:30.660][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:14:30.661][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:14:30.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.666][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:14:30.667][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:14:30.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.670][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 16:14:30.671][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:14:30.672][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:14:30.674][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:14:30.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.678][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:14:30.679][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:14:30.681][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:14:30.682][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:14:30.683][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:14:30.684][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:14:30.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.689][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:14:30.690][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:14:30.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.694][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:14:30.696][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:14:30.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.700][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:14:30.701][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:14:30.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.706][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:14:30.707][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:14:30.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.710][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 16:14:30.711][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:14:30.712][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:14:30.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.717][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:14:30.718][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:14:30.722][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:14:30.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.726][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:14:30.727][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:14:30.729][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:14:30.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.735][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:14:30.762][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.775][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-22 16:14:30.777][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.778][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:30.779][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.780][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.782][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.783][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.784][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:14:30.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:30.787][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.788][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:14:30.789][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:30.790][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.791][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.793][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:14:30.793][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:14:30.793][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:14:30.793][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:14:30.793][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:14:30.794][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:14:30.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:30.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:30.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:30.799][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:30.800][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:30.801][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.807][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.809][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:30.810][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:30.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.812][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.813][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:14:30.815][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.816][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:14:30.818][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.819][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:30.820][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.822][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.825][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:14:30.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:30.827][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.828][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:14:30.829][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:30.831][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.832][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.833][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:14:30.833][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:14:30.833][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:14:30.833][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:14:30.833][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:14:30.834][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:14:30.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:30.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:30.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:30.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:30.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:30.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.843][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:30.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:30.846][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.847][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.848][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:14:30.850][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.852][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-22 16:14:30.853][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.854][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:30.855][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.859][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.860][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.861][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.862][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:14:30.864][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:30.865][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.866][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:14:30.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:30.869][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.870][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.871][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.872][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:14:30.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:30.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:30.876][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:30.877][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:30.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:30.879][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.880][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.881][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:30.882][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:30.884][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.885][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.886][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:14:30.888][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.889][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:14:30.890][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:30.893][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.894][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.895][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.896][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.898][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:14:30.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:30.900][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.901][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:14:30.902][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:30.904][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.905][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:30.906][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.907][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:14:30.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:30.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:30.911][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:30.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:30.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:30.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:30.915][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.916][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:30.918][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:30.919][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:30.920][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:30.923][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:14:30.924][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:30.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:30.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.940][FUN] 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 16:14:30.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.942][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 16:14:30.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.945][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 16:14:30.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.947][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 16:14:30.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.950][FUN] 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 16:14:30.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.956][FUN] 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 16:14:30.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.961][FUN] 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 16:14:30.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.967][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 16:14:30.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.969][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 16:14:30.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.972][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 16:14:30.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.977][FUN] 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 16:14:30.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.983][FUN] 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 16:14:30.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:30.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.988][FUN] 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 16:14:30.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.993][FUN] 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 16:14:30.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:30.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:30.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:30.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:30.999][FUN] 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 16:14:31.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.004][FUN] 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 16:14:31.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:31.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.009][FUN] 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 16:14:31.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.015][FUN] 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 16:14:31.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:31.019][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:14:31.028][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:14:31.029][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:14:31.031][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:14:31.032][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:14:31.034][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:14:31.035][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:14:31.037][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:14:31.038][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:14:31.040][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:14:31.041][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:14:31.043][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:14:31.045][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:14:31.046][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:14:31.048][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:14:31.049][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:14:31.051][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:14:31.052][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:14:31.054][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:14:31.055][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:14:31.057][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:14:31.059][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:14:31.060][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:14:31.062][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:14:31.063][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:14:31.065][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:14:31.066][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:14:31.068][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:14:31.070][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:14:31.071][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:14:31.073][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:14:31.074][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:14:31.076][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:14:31.077][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:14:31.079][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:14:31.080][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:14:31.082][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:14:31.083][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:14:31.085][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:14:31.086][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:14:31.088][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:14:31.090][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:14:31.091][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:14:31.093][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:14:31.094][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:14:31.096][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:14:31.097][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:14:31.099][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:14:31.101][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:14:31.102][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:14:31.104][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:14:31.105][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:14:31.107][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:14:31.108][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:14:31.110][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:14:31.111][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:14:31.113][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:14:31.114][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:14:31.116][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:14:31.118][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:14:31.119][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:14:31.121][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:14:31.122][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:14:31.124][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:14:31.125][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:14:31.127][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:14:31.128][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:14:31.130][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:14:31.132][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:14:31.133][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:14:31.135][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:14:31.136][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:14:31.138][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:14:31.139][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:14:31.141][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:14:31.142][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:14:31.144][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:14:31.146][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:14:31.147][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:14:31.149][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:14:31.150][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:14:31.152][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:14:31.153][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:14:31.191][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:14:31.194][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:14:31.197][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:14:31.198][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.199][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 16:14:31.200][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.201][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 16:14:31.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.210][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 16:14:31.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.212][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 16:14:31.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:31.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:31.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:31.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:31.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.233][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 16:14:31.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.235][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 16:14:31.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.241][FUN] 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 16:14:31.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:31.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:31.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:31.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.269][FUN] 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 16:14:31.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.277][FUN] 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 16:14:31.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.279][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 16:14:31.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.284][FUN] 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 16:14:31.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:31.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.292][FUN] 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 16:14:31.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.300][FUN] 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 16:14:31.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:31.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.307][FUN] 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 16:14:31.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.309][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 16:14:31.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.315][FUN] 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 16:14:31.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.323][FUN] 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 16:14:31.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:31.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:31.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:31.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.338][FUN] 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 16:14:31.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:31.344][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-22 16:14:31.353][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:14:31.356][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:31.357][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-22 16:14:31.358][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:31.359][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:31.360][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:31.362][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:31.363][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:31.364][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:31.365][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-22 16:14:31.366][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:31.368][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:31.369][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-22 16:14:31.370][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:31.371][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-22 16:14:31.371][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:14:31.371][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:14:31.371][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:14:31.373][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:31.374][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:14:31.375][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:14:31.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:31.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:31.378][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:31.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:31.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:31.382][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:31.383][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:14:31.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:31.385][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:31.386][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:31.388][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:31.394][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:14:31.417][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:14:31.418][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-22 16:14:31.422][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:14:31.425][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-22 16:14:31.429][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:14:31.430][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:14:31.431][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-22 16:14:31.443][biodb::testThat]
biodb.INFO [2024-06-22 16:14:31.444][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-22 16:14:31.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:31.447][biodb::testThat]
biodb.TRACE[2024-06-22 16:14:31.453][loadFileContents] Loaded 1 files from cache: [1]: "F:/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 16:14:31.455][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:14:31.458][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:14:31.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:14:31.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:31.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:31.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:31.496][FUN] 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 16:14:31.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:31.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:14:31.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:31.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:31.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.535][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:31.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:31.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.550][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:31.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:31.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.560][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:14:31.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.565][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.570][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.575][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.580][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:14:31.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:31.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:31.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:31.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:31.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:31.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:31.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:31.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:31.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:31.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:31.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:31.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.687][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:31.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:31.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.692][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:31.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:31.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:31.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:31.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.701][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:31.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:31.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:31.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:31.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:31.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:31.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:31.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:31.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:31.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:31.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:31.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:31.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:31.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:31.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:14:31.735][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-22 16:14:31.739][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:14:31.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:14:31.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:14:31.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:14:31.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.748][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:14:31.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:14:31.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:14:31.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:14:31.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:31.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.055][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.103][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.108][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.113][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.144][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.146][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.148][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.179][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.180][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.183][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.199][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.204][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.209][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.214][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.215][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.218][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.219][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.234][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.239][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.244][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.249][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.250][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.252][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.254][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.274][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.275][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.277][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.284][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.286][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.288][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.295][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.296][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.299][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.305][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.307][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.309][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.329][loadFileContents] Loaded 1 files from cache: [1]: "F:/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 16:14:32.358][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:14:32.360][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:14:32.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:14:32.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:32.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:32.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:32.372][FUN] 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 16:14:32.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:32.374][FUN] Functions in observer BiodbConfig: [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 16:14:32.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.382][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.392][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:14:32.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:32.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.397][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.402][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.411][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:14:32.450][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-22 16:14:32.468][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:14:32.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:14:32.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.473][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:14:32.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:14:32.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.478][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:14:32.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:14:32.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.483][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:14:32.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:14:32.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.500][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.542][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.547][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.552][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:32.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.595][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.596][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.598][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.625][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.629][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.631][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.633][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.649][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.654][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.659][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.664][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.665][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.668][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.669][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.684][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:32.685][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:32.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.688][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.695][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.696][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:32.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.698][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:32.705][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:32.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:32.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:32.709][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:14:32.721][biodb::testThat]
biodb.INFO [2024-06-22 16:14:32.723][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-22 16:14:32.724][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:32.725][biodb::testThat]
biodb.DEBUG[2024-06-22 16:14:32.728][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-22 16:14:32.735][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-22 16:14:32.744][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-22 16:14:32.747][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-22 16:14:32.749][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-22 16:14:32.750][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-22 16:14:32.752][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-22 16:14:32.753][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:14:32.754][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-22 16:14:32.755][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-22 16:14:32.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:14:32.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:32.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:32.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:32.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:32.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:32.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:32.781][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-22 16:14:32.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:14:32.801][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:14:32.803][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-22 16:14:33.680][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-06-22 16:14:33.682][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-22 16:14:33.683][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-22 16:14:33.684][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-22 16:14:34.087][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:14:34.090][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-22 16:14:34.104][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-22 16:14:34.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:14:34.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:34.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:34.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:34.119][FUN] 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 16:14:34.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:34.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:34.139][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-22 16:14:34.153][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:14:34.155][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:14:34.174][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-22 16:14:34.387][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2024-06-22 16:14:34.389][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-22 16:14:34.391][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-22 16:14:34.392][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-22 16:14:34.789][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:14:34.792][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-22 16:14:34.797][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-22 16:14:34.801][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-06-22 16:14:34.804][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-22 16:14:34.806][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-22 16:14:34.807][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:14:34.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:14:34.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:34.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:34.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:34.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:34.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:34.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:14:34.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.830][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:34.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:34.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.835][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:34.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:34.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.840][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:14:34.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:34.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:34.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:34.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:34.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:34.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:34.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:34.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:34.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:34.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:34.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:34.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.870][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.875][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.885][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:14:34.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:14:34.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:34.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:34.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:34.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:34.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:34.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:14:34.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.930][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:34.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:14:34.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:34.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:34.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.941][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:14:34.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:14:34.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.950][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.960][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:14:34.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:34.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:34.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:35.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:35.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:14:35.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:14:35.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:14:35.009][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-22 16:14:35.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:14:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:14:35.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:14:35.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:14:35.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:14:35.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:14:35.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:14:35.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:14:35.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:14:35.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:14:35.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:14:35.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:14:35.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:14:35.062][biodb::testThat]
biodb.INFO [2024-06-22 16:14:35.064][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-22 16:14:35.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:35.066][biodb::testThat]
biodb.TRACE[2024-06-22 16:14:35.070][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:35.071][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:35.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.073][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:14:35.075][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-22 16:14:35.105][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:35.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:35.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:35.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:35.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:35.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:35.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:14:35.123][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:14:35.125][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:14:35.129][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:14:35.130][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:14:35.131][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-22 16:14:35.342][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2024-06-22 16:14:35.344][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-22 16:14:35.345][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-22 16:14:35.347][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-22 16:14:35.770][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:14:35.773][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-22 16:14:35.778][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-22 16:14:35.784][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-22 16:14:35.809][biodb::testThat]
biodb.INFO [2024-06-22 16:14:35.810][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-22 16:14:35.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:35.813][biodb::testThat]
biodb.TRACE[2024-06-22 16:14:35.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:35.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:35.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:35.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:35.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:35.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:35.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:14:35.888][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:14:35.891][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-22 16:14:35.905][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-22 16:14:35.907][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-22 16:14:35.912][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-22 16:14:35.939][biodb::testThat]
biodb.INFO [2024-06-22 16:14:35.941][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-22 16:14:35.942][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:35.943][biodb::testThat]
biodb.TRACE[2024-06-22 16:14:35.961][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:14:35.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:14:35.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.966][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:14:35.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:14:35.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.971][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:14:35.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:14:35.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:35.976][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:14:35.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:14:35.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:35.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:36.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:14:36.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:14:36.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:36.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:36.014][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:14:36.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:14:36.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:36.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:36.019][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:14:36.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:14:36.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:36.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:36.024][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:14:36.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:14:36.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:36.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:14:36.037][biodb::testThat]
biodb.INFO [2024-06-22 16:14:36.039][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-22 16:14:36.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:36.041][biodb::testThat]
biodb.INFO [2024-06-22 16:14:36.053][biodb::testThat]
biodb.INFO [2024-06-22 16:14:36.055][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-22 16:14:36.056][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:36.057][biodb::testThat]
biodb.INFO [2024-06-22 16:14:36.073][biodb::testThat]
biodb.INFO [2024-06-22 16:14:36.074][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-22 16:14:36.076][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:36.077][biodb::testThat]
biodb.DEBUG[2024-06-22 16:14:36.090][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 16:14:36.309][getUrlContent] Use base::url() 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 16:14:36.745][biodb::testThat]
biodb.INFO [2024-06-22 16:14:36.747][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-22 16:14:36.748][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:14:36.749][biodb::testThat]
biodb.DEBUG[2024-06-22 16:14:36.967][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 16:14:37.489][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:37.491][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:37.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:37.493][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:14:37.495][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:14:37.496][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:14:37.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:14:37.498][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:14:37.499][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:14:37.501][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-22 16:14:37.502][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-22 16:14:37.503][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:14:37.504][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:37.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:37.507][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:37.509][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-22 16:14:37.520][biodb::testContext]
biodb.INFO [2024-06-22 16:14:37.521][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:14:37.522][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-22 16:14:37.524][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:14:37.525][biodb::testContext]
biodb.INFO [2024-06-22 16:14:37.529][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:14:37.532][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:14:37.537][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:14:37.539][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:14:37.540][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:14:37.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.550][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:14:37.551][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:14:37.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.556][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:14:37.557][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:14:37.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.561][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:14:37.563][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:14:37.564][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:14:37.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.568][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:14:37.569][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:14:37.571][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:14:37.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.575][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:14:37.576][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:14:37.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.581][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:14:37.582][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:14:37.583][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:14:37.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.587][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 16:14:37.588][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:14:37.589][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:14:37.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.593][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:14:37.595][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:14:37.596][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:14:37.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.600][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:14:37.601][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:14:37.603][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:14:37.604][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:14:37.605][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:14:37.606][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:14:37.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.611][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:14:37.612][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:14:37.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.616][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:14:37.618][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:14:37.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.622][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:14:37.623][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:14:37.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.628][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:14:37.629][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:14:37.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.633][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:14:37.635][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:14:37.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.638][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 16:14:37.639][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:14:37.640][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:14:37.644][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:14:37.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.648][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:14:37.649][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:14:37.651][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:14:37.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.654][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 16:14:37.655][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:14:37.657][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.659][self$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 16:14:37.660][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.661][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:37.662][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.663][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.665][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.666][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.667][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:14:37.668][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:37.674][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.675][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:14:37.677][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:37.678][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.679][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.680][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:14:37.680][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:14:37.680][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:14:37.680][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:14:37.680][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:14:37.681][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:14:37.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:37.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:37.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:37.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:37.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:37.688][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.689][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.691][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:37.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:37.693][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.694][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.695][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:14:37.697][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.699][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:14:37.700][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.701][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:37.702][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.703][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.704][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.706][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.707][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:14:37.708][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:37.709][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.711][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:14:37.712][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:37.713][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.714][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.715][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:14:37.715][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:14:37.715][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:14:37.715][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:14:37.715][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:14:37.717][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:14:37.718][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:37.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:37.720][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:37.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:37.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:37.723][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.725][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.726][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:37.727][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:37.728][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.729][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.731][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:14:37.733][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.734][self$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 16:14:37.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.736][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:37.737][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.739][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.740][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.741][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.742][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:14:37.743][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:37.745][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.746][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:14:37.747][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:37.748][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.749][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.750][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.752][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:14:37.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:37.754][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:37.755][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:37.756][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:37.757][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:37.758][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.760][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.761][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:37.762][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:37.763][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.764][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.766][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:14:37.768][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.769][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:14:37.770][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.771][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:37.772][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.773][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.775][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.776][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.777][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:14:37.778][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:37.779][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.781][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:14:37.782][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:37.783][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.784][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:37.785][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.787][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:14:37.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:37.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:37.795][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:37.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:37.797][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:37.798][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:37.799][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.800][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:37.801][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:37.803][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:37.804][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:37.805][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:14:37.806][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:37.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.816][FUN] 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 16:14:37.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.821][FUN] 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 16:14:37.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.827][FUN] 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 16:14:37.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.832][FUN] 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 16:14:37.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.838][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 16:14:37.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.843][FUN] 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 16:14:37.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:37.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:37.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:37.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.865][FUN] 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 16:14:37.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.870][FUN] 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 16:14:37.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.876][FUN] 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 16:14:37.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.881][FUN] 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 16:14:37.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.887][FUN] 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 16:14:37.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.892][FUN] 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 16:14:37.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:37.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:37.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:37.898][FUN] 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 16:14:37.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:37.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:37.901][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:14:37.903][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:14:37.904][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:14:37.906][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:14:37.907][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:14:37.909][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:14:37.915][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:14:37.917][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:14:37.918][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:14:37.920][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:14:37.921][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:14:37.923][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:14:37.924][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:14:37.926][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:14:37.927][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:14:37.929][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:14:37.930][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:14:37.932][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:14:37.933][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:14:37.935][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:14:37.937][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:14:37.938][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:14:37.940][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:14:37.941][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:14:37.943][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:14:37.944][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:14:37.946][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:14:37.948][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:14:37.949][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:14:37.951][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:14:37.952][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:14:37.954][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:14:37.955][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:14:37.957][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:14:37.958][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:14:37.960][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:14:37.962][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:14:37.963][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:14:37.965][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:14:37.966][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:14:37.968][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:14:37.969][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:14:37.971][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:14:37.972][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:14:37.974][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:14:37.976][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:14:37.977][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:14:37.979][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:14:37.980][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:14:37.982][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:14:37.983][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:14:37.985][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:14:37.986][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:14:37.988][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:14:37.990][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:14:37.991][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:14:37.993][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:14:37.994][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:14:37.996][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:14:37.997][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:14:37.999][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:14:38.000][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:14:38.002][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:14:38.003][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:14:38.005][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:14:38.007][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:14:38.008][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:14:38.010][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:14:38.011][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:14:38.013][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:14:38.014][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:14:38.016][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:14:38.017][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:14:38.024][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:14:38.026][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:14:38.027][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:14:38.029][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:14:38.030][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:14:38.032][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:14:38.033][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:14:38.035][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:14:38.036][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:14:38.038][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:14:38.039][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:14:38.042][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:14:38.043][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:14:38.045][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.046][FUN] 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 16:14:38.047][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.053][FUN] 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 16:14:38.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.061][FUN] 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 16:14:38.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.069][FUN] 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 16:14:38.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:38.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.076][FUN] 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 16:14:38.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.084][FUN] 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 16:14:38.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.091][FUN] 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 16:14:38.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.099][FUN] 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 16:14:38.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.106][FUN] 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 16:14:38.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:38.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.114][FUN] 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 16:14:38.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.121][FUN] 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 16:14:38.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.129][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 16:14:38.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.131][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 16:14:38.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.137][FUN] 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 16:14:38.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:38.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.149][FUN] 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 16:14:38.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.157][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 16:14:38.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.159][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 16:14:38.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:38.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:14:38.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.172][FUN] 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 16:14:38.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:14:38.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.180][FUN] 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 16:14:38.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:14:38.186][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-22 16:14:38.188][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:14:38.190][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:38.191][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-22 16:14:38.192][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:38.193][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:14:38.195][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:38.196][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:14:38.197][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:38.198][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:14:38.199][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-22 16:14:38.201][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:14:38.202][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:38.203][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-22 16:14:38.204][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:14:38.206][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-22 16:14:38.206][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:14:38.206][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:14:38.206][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:14:38.207][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:14:38.208][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:14:38.209][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:14:38.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:38.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:38.213][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:14:38.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:14:38.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:14:38.216][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:14:38.217][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:14:38.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:14:38.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:14:38.221][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:14:38.222][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:14:38.223][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:14:38.227][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:14:38.228][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-22 16:14:38.229][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:14:38.231][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-22 16:14:38.233][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:14:38.234][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:14:38.235][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-22 16:14:38.236][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:14:38.238][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-22 16:14:38.239][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-22 16:14:38.240][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:14:38.241][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:14:38.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:14:38.243][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:14:38.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:14:38.245][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:14:38.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --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 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'biodbExpasy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/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)